Method of detecting ivermectin sensitivity in a canine subject by identifying a mutation in a mdr1-encoding sequence

ABSTRACT

This invention provides the identification of a truncation polymorphism of the mdr1 gene that is linked to ivermectin sensitivity in subjects, such as collies. Also provided are methods for detecting drug transport sensitivity in a subject, and animal models and in vitro cell systems using cells from animals having an mdr1 truncation.

REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional applications No. 60/261,578 (filed Jan. 12, 2001) and No. 60/314,829 (filed Aug. 24, 2001), both of which are incorporated herein by reference in their entirety.

FIELD

This disclosure relates to methods and kits for detecting a subject's sensitivity to pharmaceutical agents, particularly an animal's sensitivity to application of drugs (such as ivermectin) that interact with P-glycoprotein. It also relates to variants of the mdr1 gene, which variants impact transport of drugs that interact with the P-glycoprotein, as well as cell and whole animal systems comprising such variants and methods of using these systems.

BACKGROUND

The observation, over 100 years ago, that certain chemical dyes injected into the peripheral circulation were able to gain access to most organs but not the brain led to the concept of a blood-brain barrier. Research in the 1960's demonstrated that the anatomical basis of the blood-brain barrier is the specialized endothelial cells of brain capillaries. While it has been thought that the entry of drugs, toxins, and xenobiotics into the brain is simply a function of lipophilicity, electrical charge, and molecular weight, ongoing research demonstrates that the capillary endothelium composing the blood-brain barrier is not simply an anatomic entity. A number of active transport systems exist that selectively regulate both influx and efflux of compounds across brain capillary endothelial cells. The most important drug-efflux system of the blood-brain barrier identified to date is P-glycoprotein.

P-glycoprotein, the product of the mdr1 (multidrug resistance) gene, is a 170-kD membrane-spanning, cell-surface protein that functions as a drug-efflux pump. P-glycoprotein was first identified over 20 years ago in chemotherapeutic drug-resistant tumor cells, and is now known to be a major cause of multidrug resistance in human and veterinary cancer patients. In tumor cells, P-glycoprotein functions as an ATP-dependent efflux pump resulting in decreased intracellular drug accumulation and reduced cytotoxicity. Chemotherapeutic drugs that are substrates for P-glycoprotein include Vinca alkaloids (vincristine and vinblastine), doxorubicin and related compounds, taxanes, and epipodophyllotoxins. Alkylating agents, platinum compounds, and antimetabolites are not substrates for P-glycoprotein. Though these agents are structurally and functionally dissimilar, P-glycoprotein substrates share several other characteristics. They typically are complex, hydrophobic, amphipathic compounds that are natural products (i.e., derived from plants or micro-organisms) or analogs of natural products. A number of non-cytotoxic compounds have been identified as P-glycoprotein substrates, including steroid hormones, bilirubin, antiparasitic agents, selected antimicrobial agents, and others.

P-glycoprotein is expressed not only in tumor cells, but also in a variety of normal tissues, including renal tubular epithelium, canalicular surfaces of hepatocytes, adrenal cortical cells, colonic and intestinal epithelium, placenta, apical margins of bronchiolar epithelium, and brain capillary endothelial cells. Consistent with its function as a transport pump, the expression of P-glycoprotein in non-neoplastic tissues suggests a normal physiologic role for P-glycoprotein mediating the export of potentially toxic xenobiotics from the body. Although the normal function of P-glycoprotein in many of these tissues has not been elucidated, a great deal is known about its role in the blood-brain barrier.

Avermectins are a class of natural products with broad antiparasitic activity. Ivermectin, a semi-synthetic lactone in the avermectin family, is a drug that is used extensively in veterinary medicine to treat and control infections caused by nematode and arthropod parasites. It is also used in human medicine to treat onchocerciasis, lymphatic filariasis, and strongyloidiasis. Ivermectin induces a tonic paralysis in invertebrate organisms by potentiating glutamate-gated chloride channels, and/or gamma-amino butyric acid (GABA)-gated chloride channels (Tracy and Webster, In: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9^(th) edition. Hardman et al., eds. New York: McGraw-Hill, 1996: 1009-1026, 1996) of the peripheral nervous system. In most mammals, the blood-brain barrier prevents access of ivermectin to the central nervous system, and since GABA receptors in mammals are restricted to sites within the central nervous system, mammals are generally protected from the neurologic effects of ivermectin (Fisher and Mrozik, Annu. Rev. Pharmacol. Toxicol. 32:537-553, 1992).

There are some specific subgroups of mice and dogs, however, that are exquisitely sensitive to the neurologic actions of ivermectin. Genetically engineered mdr1a knock-out [mdr1a(-/-)] mice are 50 to 100 times more sensitive to ivermectin-mediated neurotoxicity than wild-type mice (Schinkel et al., Cell. 77:491-502, 1994), and accumulate 80-90-fold higher concentrations of ivermectin in the brain than do wild-type mice. The protein product of mdr1a, called P-glycoprotein (P-gp) is a 170-kD transmembrane protein pump that is present at high concentrations in the apical membrane of brain capillary endothelial cells (Van Asperen et al., J. Pharmaceut. Sci. 86:881-884, 1997, 1997; Tsuji, Therap. Drug Monitor. 20:588-590, 1998). Substrates of P-gp include a variety of large, structurally unrelated hydrophobic compounds, including naturally occurring compounds such as ivermectin, cyclosporin, digoxin, and others. After substrates are bound by P-gp, they are actively extruded from the endothelial cell into the capillary lumen (Van Asperen et al., J. Pharmaceut. Sci. 86:881-884, 1997). Abrogation of P-gp results in failure of the blood-brain barrier. High concentrations of ivermectin accumulate in brain tissue from mdr1a (-/-) mice, and neurotoxicity ensues.

Approximately 25% of a population of the CF-1 mouse strain were much more sensitive to neurotoxicity produced by ivermectin than unaffected mice of the same strain (Umbenhauer et al., Toxicol Appl. Pharmacol. 146:88-94, 1997). Investigation into the cause of this sensitivity led to the discovery that the sensitive animals did not express P-gp in their brain endothelial cells. Furthermore, a restriction-fragment-length polymorphism in the murine mdr gene was documented that allowed prediction of sensitive animals, and an inheritance pattern following normal Mendelian genetics was observed (Umbenhauer et al., Toxicol Appl. Pharmacol. 146:88-94, 1997).

In dogs, a breed-related sensitivity to ivermectin has been reported in Collies, that may affect 30 to 50% of the population (Pulliam et al., Veter. Med. 7:33-40, 1985; Hsu et al., Comp. Contin. Educat. Veter. Pract. 11:584-589, 1989, Paul et al., Am. J. Vet. Res. 48:685-688, 1987). In one study, 1/200^(th) of the lethal dose of ivermectin for Beagles was lethal for Collies (Pulliam et al., Veter. Med. 7:33-40, 1985). Other related canine breeds believed to be affected by ivermectin sensitivity include Border Collies, Shetland Sheepdogs, Old English Sheepdogs, and Australian Shepherds (Campbell and Benz, J. Vet. Pharmacol. Therap. 7:1-16, 1984).

Despite numerous investigations (Vaughn, et al., Vet. Res. Commun. 13:47-55, 1989; Roher et al., Vet. Res. Commun. 14:157-165, 1990; Pulliam et al., Veter. Med. 7:33-40, 1985), the mechanism for ivermectin-sensitivity in Collies is unknown.

SUMMARY OF THE DISCLOSURE

The disclosure provides a mutation in the mdr1 gene, which results in production of truncated and non-functional P-gp and thereby causes sensitivity to ivermectin and other drugs that serve as P-gp substrates. With the identification of this mutation, methods are provided to determine if an individual subject is sensitive to ivermectin. Also provided are systems for examining the importance of P-gp in drug transport in whole animal and cell culture systems.

A provided embodiment is a method of detecting ivermectin sensitivity in a subject (for instance a mammal, such as a canine animal), which method includes determining whether a gene-truncation mutation in a mdr1-encoding sequence of the subject or a truncated P-pg is present in the subject. Such a gene-truncation mutation or truncation of P-gp indicates that the subject is sensitive to ivermectin. In specific examples of such methods, the gene truncation mutation is a deletion of about four base pairs at about residue 294-297 of SEQ ID NO: 1 (the canine mdr1 cDNA) or a homologous cDNA or gene.

In certain embodiments, methods provided herein are used to evaluate whether the subject can be treated safely with ivermectin or another drug that can be excluded from the brain by P-gp (such as those listed in Table 2).

In certain provided methods, the method includes determining whether the subject is homozygous or heterozygous for the gene-truncation mutation.

In specific examples of the provided methods, determining whether a gene-truncation mutation is present in the subject includes subjecting DNA or RNA from the subject to amplification using oligonucleotide primers, for instance in performing an oligonucleotide ligation assay.

In a specific embodiment provided herein, the method of detecting ivermectin sensitivity in a subject involves obtaining a test sample of DNA containing a mdr1 sequence of the subject; and determining whether the subject has the gene-truncation mutation in the mdr1 sequence, wherein the presence of the mutation indicates sensitivity to ivermectin. In certain examples of this embodiment, determining whether the subject has the mutation comprises using restriction digestion, probe hybridization, nucleic acid amplification, or nucleotide sequencing.

Further embodiments of methods provided herein involve obtaining from the subject a test sample of DNA comprising an mdr1 sequence; contacting the test sample with at least one nucleic acid probe for an mdr1 gene truncation mutation that is associated with ivermectin sensitivity, to form a hybridization sample; maintaining the hybridization sample under conditions sufficient for specific hybridization of the mdr1 sequence with the nucleic acid probe; and detecting whether the mdr1 sequence specifically hybridizes with the nucleic acid probe, wherein specific hybridization of the mdr1 sequence with the nucleic acid probe indicates ivermectin sensitivity. In specific examples of such embodiments, the probe is present on a substrate, for instance a nucleotide array.

Also provided are methods of detecting ivermectin sensitivity in a subject by determining whether truncated P-gp is present in a sample from the subject. Certain examples of such methods will involve reacting at least one P-gp molecule contained in the sample from the subject with a P-gp-specific binding agent (such as an antibody) to form a P-gp:agent complex. Such methods can further include detecting the P-gp:agent complex, for instance by Western blot assay, ELISA, or other immunoassay technique.

Also provided herein are kits for use in diagnosing ivermectin sensitivity in a subject. Such kits include at least one probe that specifically hybridizes to an mdr1 gene-truncation mutation associated with ivermectin sensitivity. In specific examples of such kits, the probe specifically hybridizes to an mdr1 gene-truncation mutation at or about residue 294-297 of SEQ ID NO: 1.

Other provided kits for use in diagnosing ivermectin sensitivity in a subject contain a P-gp-specific binding agent, such as an antibody. In specific examples of such kits, the provided agent is capable of specifically binding to truncated P-gp protein.

Also provided herein are oligonucleotides that specifically hybridize to a canine mdr1 gene-truncation mutation, for instance an oligonucleotide that hybridizes to an mdr1 gene-truncation mutation at residue 294-297.

Other embodiments are systems and methods for studying the effects of drugs (and drug candidates) on biological systems expressing a mdr1 gene truncation, such as the mdr1 gene-truncation mutation at residues 294-297. Examples of such systems include cultured cells (such as intestinal epithelial cells, brain endothelial cells (for instance, capillary endothelial cells), renal-tubular cells, hepatocytes, or neoplastic cells) isolated from a canine that naturally exhibits a gene truncation mutation in the mdr1 gene. Other examples of such systems include animal models (including for instance dogs) in which the mdr1 gene is naturally truncated, or in which such truncations have been engineered using recombinant technologies and/or cloning. Methods are also provided for using these animal models and cell systems, for instance to study drug interactions with P-gp or to examine the impact of drugs and drug candidates on biological systems. Such methods would be particularly useful in the drug approval process.

One embodiment is a method of determining a P-gp influenced biological effect of a compound on a canine cellular system, which method involves contacting a canine cell having a truncation mutation in its mdr1 gene with the compound, and comparing a characteristic (such as a genetic, physiological, chemical, or morphological characteristic) of the canine cell contacted with the compound with the characteristic of a similar canine cell that was not contacted with the compound. In such methods, a difference in the characteristic between the two cells is indicative of the P-gp influenced biological effect in the cell. In specific examples of such methods, the canine cell is a Collie cell. The truncation mutation in the mdr1 gene is in some examples a mutation at residue 294-297.

Specific types of canine cells include, but are not limited to, gastrointestinal tissue cells, renal tissue cells, nerve tissue cells, brain capillary endothelial cells, and liver tissue cells. In some methods, the canine cell is a neoplastic cell.

Also provided are methods of determining a P-gp influenced biological effect of a compound on a canine cellular system, wherein contacting the canine cell with the compound occurs in vivo in the native environment of the canine cell, for instance in a dog (such as a Collie dog).

In some examples of the provided methods, biological effects include absorption or distribution of a drug or compound, for instance a drug or compound that interacts with or is transported by P-gp.

Also provided is an animal model useful for studying a P-gp influenced biological effect of a compound, comprising a Collie identified as being homozygous or heterozygous for a truncation mutation in the mdr1 gene (for instance, a mutation at residue 294-297). Also provided are methods of using this animal model to examine the effect of compounds that interact with P-gp, for instance compounds that are transported by P-gp or that modulate its transport activity.

Compounds contemplated for use in the methods provided herein include anti-infective agents (e.g., antiviral, antibacterial, or anti-prion agents), antineoplastic agents, analgesics, neurokinin receptor antagonists, anti-emetic agents, beta-adrenergic receptor antagonists, antiepileptic agents, anti-psychotic agents, anti-depressive agents, and other drugs that act on the central nervous system.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is a semi-quantitative reverse transcriptase PCR analysis of mdr1 in blood samples from ivermectin-sensitive (samples 15 and 16) and non-sensitive (resistant) (samples 17 and 18) Collies. Duplicate reactions were assayed for each dog as shown using canine mdr1 and GAPDH primers. The resultant amplicons were separated by electrophoresis through an agarose gel. The arrows indicate the expected size of the mdr1 (P-gp) and GAPDH products.

FIG. 1B is a graph, quantitating the UV fluorescence of mdr1 and GAPDH reverse transcriptase PCR products obtained by digital image analysis of the ethidium bromide-stained gel shown in FIG. 1A.

FIG. 2 is a sequence comparison of wild-type (top) and mutant (bottom) mdr1 cDNAs. As demonstrated herein, a four base pair deletion is present in the mutant cDNA. Codons in the vicinity of the deletion are indicated by brackets for both the wildtype and mutant cDNAs. Bolded letters indicate stop codons created in the mutant cDNA as a result of the frame-shift. The dashed box indicates the palindromic sequence in the vicinity of the deletion mutation.

FIG. 3 is a diagrammatic representation of the transmembrane structure of P-gp (Gottesman and Pastan, Annu. Rev. Biochem. 62:385-427, 1993). The mutation site (arrowhead) occurs at amino acid 75, resulting in a frame shift that generates several downstream stop codons, the first two of which occur at amino acid positions 91 and 111. Greater than 90% of the protein is predicted to be missing in dogs homozygous for the mutant allele due to the truncation.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three-letter code for amino acids, as defined in 37 C.F.R. §1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NO: 1 shows the nucleotide sequence of the canine mdr1 CDNA (GenBank Accession No. AF045016), and the P-gp amino acid sequence encoded thereby.

SEQ ID NO: 2 shows the amino acid sequence of canine P-gp.

SEQ ID NOs: 3-10 show respective synthetic oligonucleotides used to primer in vitro amplification reactions of the canine mdr1 gene, as described in Example 1.

DETAILED DESCRIPTION

I. Abbreviations

mdr multidrug resistance gene

P-gp P-glycoprotein, protein product of the mdr1 gene

II. Terms

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes VII, published by Oxford University Press, 2000 (ISBN 0-19-879276-X); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

Unless otherwise explained herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

III. Identification of Truncation Mutations in mdr1, Responsible for Collie Sensitivity to Ivermectin

There is a sub-population of Collies and dogs of related breeds that display a similar sensitivity to ivermectin. The inventors have surprisingly discovered that a deletion mutation of the mdr1 gene exists in ivermectin-sensitive Collies. The mutation produces a frame shift that generates a premature stop codon in the mdr1 gene resulting in a severely truncated, nonfunctional protein. Collies homozygous for the deletion (mutant/mutant) exhibit ivermectin sensitivity while those that are heterozygous (normal/mutant) or homozygous normal are not sensitive to ivermectin neurotoxicity. Several other breeds, including Australian shepherds, Shelties, and Old English Sheepdogs have been reported to exhibit ivermectin sensitivity; it is believed that susceptible individuals of these species may also display truncation mutations in the mdr1 gene.

The identification of the naturally occurring mdr1 truncation mutations in dogs has enabled the use of animals carrying such a mutation, and of cells derived from such animals, to study interactions of drugs (or potential drugs) with P-gp and the systemic effects of such interactions. These animal and cell-based systems are particularly useful for identifying and characterizing ways to:

(a) improve, regulate, or prevent gastrointestinal absorption of drugs;

(b) improve, regulate, or prevent brain penetration of drugs (e.g., increasing brain penetration of HIV-1 drugs; drugs for treating prion diseases; antineoplastic agents; or compounds for pain or depression);

(c) improve, regulate, or prevent renal excretion of drugs;

(d) improve penetration of drugs into tumor cells;

(e) improve, regulate, or prevent biliary excretion of drugs; and

(f) improve, regulate or prevent penetration of drugs through the placenta.

These systems are also particularly useful to study the effects of functional mdr1 polymorphism(s), particularly in order to understand the effects of such polymorphisms as they may be found in additional species, including for instance humans. The systems can also be used to study the effects (drug interactions) that a highly effective, potent P-gp inhibitor would have in an intact biological system, and thus provides an excellent method for examining the large-mammal effects of drugs, for example during the drug approval and testing process.

The invention is illustrated by the following non-limiting Examples.

EXAMPLES Example 1 Identification of a Truncation Mutation in Collie mdr1 Materials and Methods

General Procedures and Materials

Procedures used in research disclosed herein were approved by the Institutional Animal Care and Use Committee.

Blood samples (8 ml) were obtained by jugular venipuncture from each of 13 clinically healthy Collies (Wil-O-Lane Kennels, Allegan, Mich.). All Collies used in the study had previously been identified as ivermectin-sensitive or -nonsensitive by observing dogs for signs of neurotoxicosis after oral administration of 120 μg of ivermectin per kg of body weight (20 times the label dose for heartworm prevention), as previously described (Paul et al, Amer. J. Vet. Res. 61:482-483, 2000; Fassler et al., J. Am. Vet. Med. Assoc. 199:457-460, 1991). Each dog was identified by an ear tattoo and housed in a run measuring 4×8 feet with metal walls and a raised, coated, metal screen floor. Facilities exceeded the minimal requirement specified by USDA guidelines.

Seven Collies were identified as ivermectin-sensitive (4 male and 3 female) and 6 were not ivermectin-sensitive (3 male and 3 female). Two of the Collies in the study were littermates and two others were non-littermate siblings. Of the two littermates, one was sensitive to ivermectin, the other was not. Both of the non-littermate siblings were sensitive to ivermectin. Several other Collies in this study shared either the same sire or the same dam. Two of the common sires and three of the common dams were represented by offspring in both the ivermectin-sensitive and -nonsensitive groups. Additional blood samples were obtained from 4 non-Collie dogs, including 1 Beagle, 2 Golden Retrievers, and 1 Staffordshire terrier cross-bred dog.

Semiquantitative RT-PCR of Canine mdr1 Gene

Total RNA was extracted from venous blood leukocytes using TRIzol reagent (Gibco BRL). Blood leukocytes were prepared by density gradient centrifugation. For RT reactions, a GeneAmp RT PCR kit (Perkin-Elmer) was used with oligo(dT) primers. Equivalent amounts of cDNA were then amplified in separate PCR reactions using Amplitaq (Perkin Elmer) with 2.5 mM MgCl₂.

PCR consisted of either 20 (GAPDH) or 27 (mdr1 product A) cycles, with denaturing, annealing, and extension conditions of 95° C. (15 seconds), 60° C. (15 seconds), and 72° C. (60 seconds) in a Perkin-Elmer thermocycler (2400 GeneAmp PCR System). The number of cycles for each product was determined on the basis of kinetic studies to ensure that the amplification reaction was within the logarithmic (not plateau) range. PCR products were resolved by electrophoresis in 1% agarose gels containing ethidium bromide. Expected sizes of the GAPDH and mdr1 A band are 229 bp and 892 bp, respectively. The UV fluorescence of DNA bands was measured with an IS-1000 Digital Imaging System (Alpha Innotec). For individual dogs, the fluorescence value for the mdr1 A product is divided by the fluorescence value of the GAPDH product to allow direct comparison between dogs.

Sequencing of Canine mdr1 cDNA

Four primer pairs, amplifying four products (referred to herein as A, B, C, and D) spanning 95% of the canine mdr1 cDNA (GenBank Accession No. AF04016) were designed for sequencing experiments (see, Table 1). Using RNA from three of the sensitive Collies, cDNA was synthesized in RT reactions as described above and amplified in separate reactions. For products A, B, and C, PCR was accomplished using the conditions described above, using 35 cycles. PCR for product D consisted of 35 cycles, with denaturing, annealing, and extension conditions of 95° C. (10 seconds), 64.5° C. (15 seconds), and 72° C. (150 seconds). Optimal MgCl₂ concentrations were 2.5 mM for PCR products A, C, and D, and 1.5 mM for PCR product B. For initial experiments, products generated from samples of three different dogs were ligated into pGEM-T Easy (ProMega), which was then used to transform ElectroMAX DH10B E. coli cells by electroporation (Gene Pulser II, BioRad). Plasmid DNA was isolated (Plasmid Mini Kit, Qiagen) and sequenced by Davis Sequencing Inc. (Davis, Calif.) using dye-terminator chemistry and an automated DNA sequencer (ABI 377, PE Applied Biosystems). For all subsequent experiments, sequencing of PCR products (Davis Sequencing Inc.) following purification (Qiaquick PCR Purification Kit, Qiagen) was performed. Sequences from experimental dogs were compared to the known canine mdr1 sequence (GenBank AF 045016; SEQ ID NO: 1).

TABLE 1 Oligonucleotide primers used in this study. The combination of primer pairs used in this study provides >95% coverage of the canine mdr1 cDNA. Mdr1 Size of product PCR designation Primer Position Product A Forward: 5′- TCC GGT TTG GTG CCT ACT TG¹ 2942-2961 892 Reverse: 5′- TGC TCC TTG ACT TTG CCA TTC² 3833-3814 B Forward: 5′- CCT CAC TAA GCG GCT TCG ATA C³ 2421-2441 1021 Reverse: 5′- AAA CAG GAT GGG CTC CTG AGA C⁴ 3441-3420 C Forward: 5′- GAG GAG GTT TGC AAT GTT TC⁵ 168-189 1061 Reverse: 5′- TCT GGT TfA TGT CCA CTC TTC G⁶ 1228-1208 D Forward: 5′- AGG CAT CCC CAA GCA TTG AAG⁷ 1112-1132 1432 Reverse: 5′- TGA GCC GCA TCA TTG GCA AG⁸ 2543-2524 ¹Corresponds to SEQ ID NO: 3. ²Corresponds to SEQ ID NO: 4. ³Corresponds to SEQ ID NO: 5. ⁴Corresponds to SEQ ID NO: 6. ⁵Corresponds to SEQ ID NO: 7. ⁶Corresponds to SEQ ID NO: 8. ⁷Corresponds to SEQ ID NO: 9. ⁸Corresponds to SEQ ID NO: 10.

Results

We took advantage of a well-defined population of ivermectin-sensitive and non-sensitive Collies (Paul et al., Amer. J. Vet. Res. 61:482-483, 2000: Fassler et al., J. Am. Vet. Med. Assoc. 199:457-460, 1991). Sensitive animals were designated as those that experienced clinical signs of neurologic toxicity after receiving a single, oral dose of ivermectin (120 μg/kg). Clinical signs of neurotoxicity that were evaluated include apparent depression, ataxia, mydriasis, salivation, or drooling (Paul et al., Amer. J. Vet. Res. 61:482-483, 2000). Semi-quantitative reverse transcriptase PCR analysis was conducted on RNA isolated from ivermectin-sensitive and non-sensitive Collies to determine if mdr1 expression is lower in sensitive Collies than in non-sensitive Collies. Amplification of a 229-bp product of the canine glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene was used as an internal standard to control for variability in reverse transcriptase and PCR reactions. FIG. 1A shows representative ethidium bromide-stained RT-PCR products of GAPDH (229 bp) and mdr1 (product A, 892 bp) from ivermectin sensitive (samples 15 and 16) and nonsensitive (samples 17 and 18) Collies. Individual UV fluorescence intensity values for GAPDH and mdr1 cDNA derived from these gels are shown in FIG. 1B. The level of mdr1 gene expression, as determined by semiquantitative reverse transcriptase PCR, did not differ between ivermectin-sensitive and non-sensitive Collies.

A reverse transcriptase PCR strategy was used to clone mdr1 cDNA from one normal dog (beagle) and 3 ivermectin-sensitive Collies. Sequence data from the beagle mdr1 cDNA was identical to that reported for normal canine mdr1 cDNA (GenBank Accession No. AF045016). Sequence analysis of clones from the three ivermectin-sensitive Collies revealed an identical four base pair deletion within the first 10% of the transcript (FIG. 2). This deletion causes a frame-shift mutation at nucleotide 294 of the transcript, which corresponds to amino acid 75 (FIG. 3). The frame shift generates several stop codons (FIG. 3), the first of which occurs at amino acid position 91 of P-gp (GenBank Accession No. AF04016; SEQ ID NO: 2). The result is a severely truncated, nonfunctional, protein.

For all subsequent experiments, a PCR-based strategy was used for sequencing mdr1 cDNA so that heterozygosity could be readily detected. The exact four-nucleotide deletion (AGAT) was detected in all (7/7) samples from ivermectin-sensitive Collies. Furthermore, these dogs were homozygous for the deletion. Samples from all non-Collie dogs (1 Beagle, 2 Golden Retrievers, and 1 Staffordshire terrier cross-bred dog) were homozygous wild-type. Interestingly, samples from all (6/6) ivermectin non-sensitive Collies displayed a heterozygous genotype, with one strand carrying the mutant allele, and the other strand carrying the wild-type allele. It is highly unlikely that these findings are a result of chance (Fisher's Exact test, P=0.006).

Discussion

The reported data demonstrate that a frame-shift deletion of four base pairs at the 5′ end of the canine mdr1 gene is associated with (and likely causes) ivermectin-sensitivity in Collies. Premature termination of P-gp synthesis as a result of the frame-shift yields a severely truncated protein that is less than one-tenth its normal size, based on the predicted amino acid sequence. P-glycoprotein's drug-efflux function is dependent upon ATP binding sites, substrate binding sites, phosphorylation sites, and multiple membrane-spanning motifs (Yoshimura et al., J. Biol. Chem. 264:16282-16291, 1989; Skach and Lingappa, Cancer Res. 54:3202-3209, 1994). Since none of these required elements are present in the truncated protein, we conclude that animals homozygous for the deletion do not express a functional form of P-gp.

The pivotal role that P-gp plays in protecting the brain from ivermectin has previously been established (Kwei et al., Drug Metab. Dispos. 27:581-587, 1999; Marques-Santos et al., Pharmacol. Toxicol. 84:125-129, 1999; Schinkel et al., J. Clin. Invest. 97:2517-2524, 1996; Van Asperen et al., J. Pharmaceut. Sci. 86:881-884, 1997). Because a large number of other drugs serve as P-gp substrates, it is possible that affected Collies would also experience greater sensitivity to the neurologic effects induced by drugs other than ivermectin. Examples of P-gp substrates that might induce neurotoxicity include those listed in Table 2 (Tsuji, Therap. Drug Monitor. 20:588-590, 1998; Schinkel et al., J. Clin. Invest. 97:2517-2524, 1996).

TABLE 2 Selected Clinically Relevant Substrates of P-glycoprotein Antineoplastic Antimicrobials and agents Antiparasitics Miscellaneous Vincristine* Cefoperazone Digoxin* Vinblastine* Tetracylines Cyclosporine A Doxorubicin* Ivermectin* Verapamil* Mitoxantrone Loperamide* Paclitaxel* Dexamethasone Ondansetron* *Drugs that have potential for neurotoxicity

In mice, people, and dogs, P-gp is normally expressed in other tissues of the body in addition to brain capillaries. Consistent with its function as a transport pump, expression of P-gp occurs at sites where it might protect the animal from xenobiotics. For example, P-gp is expressed at high levels in renal proximal tubular cells, liver, small bowel, colon, and placenta (as well as brain endothelium) (Lum et al., Pharmacother. 13:88-109, 1993; Ginn, Vet. Pathol. 33:533-541, 1993). The highest levels of P-gp expression occur in tumor cells, where P-gp functions as a multidrug transporter, protecting tumor cells from a variety of chemotherapeutic drugs including anthracyclines, Vinca alkaloids, taxanes, and epipodophyllotoxins. It is believed that ivermectin-sensitive Collies would be less likely to develop multidrug resistant tumors than the general canine population, and would therefore have better chemotherapy response rates.

The specific cause of the identified mdr1 mutation is unknown. However, it has been reported that unusual DNA structures, including palindromic DNA, promote genetic instability (Lewis et al., Ann. NY Acad. Sci. 870:45-57, 1999). Unusual DNA structures are thought to cause DNA polymerase to pause and, consequently, can disrupt DNA replication. Mutational events are not limited to sequences located within the palindromic DNA, but can also occur in sequences in the vicinity of a palindrome. Therefore, it is interesting to note that a palindromic sequence (GGTTTTTGG; FIG. 2) occurs nine bases upstream of the deletion site. Whether or not this palindromic sequence played a role in generating the four-base pair deletion in these Collies is unknown.

The inheritance pattern of ivermectin sensitivity in Collies is unknown. Results of the research described here are consistent with an autosomal recessive inheritance pattern, since only Collies that had two mutant alleles displayed the ivermectin-sensitive phenotype. However, a larger sample size will be needed to definitively determine the inheritance pattern. With many genetic diseases in people, affected individuals have many different mutations throughout the affected gene. However, in this study, all Collies had the same mutation. Because many of these animals were unrelated, it seems likely that the mutant alleles in these dogs have a common, yet-to-be-determined origin.

Example 2 Frequency of the Mutant MDR1 Allele

This Example provides methods and results from a study to determine the frequency of the mutant MDR1 allele associated with ivermectin sensitivity in a sample of Collies living in Washington and Idaho. Blood was collected from 40 Collies for RNA extraction. The RNA was reverse transcribed, and PCR performed to amplify a 1061-base pair amplicon containing the MDR1 mutation. Sequence analysis was performed to determine the genotype of each dog. Twenty-two percent of the Collies studied were homozygous for the normal allele (normal), 42% were heterozygous (carrier), and 35% were homozygous for the mutant allele (affected).

Materials and Methods

Animals—Forty clinically healthy, client-owned Collies were studied. Owner consent was obtained, and the study was approved by the Institutional Animal Care and Use Committee. Both rough-coated and smooth-coated Collies were represented. Dogs included in the sample population were those animals for which the owner was interested in determining MDR1 genotype in their pet(s). Advertising for Collies occurred primarily by announcements at the Inland Northwest Collie Club meetings and word-of-mouth. A pedigree (representing the last 4 generations) was available for eight animals.

Collection and Extraction of RNA—An 8 ml blood sample was collected from each dog for RNA isolation. Blood leukocytes were prepared by density gradient centrifugation. Total RNA was extracted from venous blood leukocytes using TRIzol reagent (Gibco BRL).

Reverse transcriptase PCR and sequencing—For reverse transcriptase reactions, a GeneAmp RT PCR kit (Perkin-Elmer) was used with oligo(dT) primers. The cDNA was then amplified (using primers as described in Example 1) in separate PCR reactions using Amplitaq (Perkin Elmer) with 2.5 mM MgCl₂. PCR consisted of 36 cycles, with denaturing, annealing, and extension conditions of 95° C. (10 seconds), 64° C. (15 seconds), and 72° C. (60 seconds) in a MJ Research thermocycler (PTC-200). PCR products were resolved by electrophoresis in 1% agarose gels containing ethidium bromide. Expected size of the MDR1 band was 1061 bp. PCR products were purified (Qiaquick PCR Purification Kit, Qiagen) and sequenced by Davis Sequencing Inc. (Davis, Calif.) using dye-terminator chemistry and an automated DNA sequencer (ABI 377, PE Applied Biosystems). Sequences from experimental dogs were compared to the known canine MDR1 sequence (GenBank AF 045016).

Results

The deletion mutation associated with ivermectin sensitivity in Collies was present in a large number of dogs in this study. Nine dogs (22%) were homozygous for the normal (wild-type) MDR1 sequence, 14 dogs (35%) were homozygous for the mutant allele, and 17 (42%) were heterozygous.

Analysis of the 8 pedigrees was performed and showed that four of the dogs in the study were closely related. For one pair of siblings, test results indicated that one dog was affected (homozygous mutant) and the other was heterozygous (one normal allele and one mutant allele). For another closely related pair of dogs, a dam and her daughter, test results indicated that the dam was heterozygous, and the daughter one dog was affected. However, there were two affected dogs that were not related to other dogs in the study within the four most recent generations. Furthermore, these eight dogs were unrelated (within the four most recent generations) to a sample population of Collies from Michigan that were studied previously, in which all animals were either heterozygous or homozygous for the described MDR1 mutation.

Discussion

Ivermectin sensitivity in Collies has recently been associated with homozygous expression of a deletion mutation of the MDR1 gene. P-glycoprotein, the product of the MDR1 gene, is an integral component of the blood-brain barrier. At the blood brain barrier, P-glycoprotein actively extrudes drugs from brain tissue back into capillaries, resulting in lower brain concentrations of drugs that are substrates for P-glycoprotein (Fromm,. Int J Clin Pharm Therap 38:69-74, 2000; Kim et al., J Clin Invest 101:289-294, 1998; Jonker et al., Br J Pharmacol 127:43-50, 1999; Schinkel, Int J Clin Pharmacol Ther 36:9-13, 1998). In MDR1 knockout mice, lack of P-glycoprotein leads to abnormally increased accumulation of certain drugs in the brain with resultant undesired neurologic adverse effects (Schinkel, Int J Clin Pharmacol Ther 36:9-13, 1998). In ivermectin-sensitive Collies, this mutation consists of a 4-base-pair deletion that generates a premature stop codon, resulting in a severely truncated, nonfunctional protein product.

Previous investigators have estimated that up to 30-40% of Collies are sensitive to ivermectin (Pulliam et al., Vet Med 80:33-40, 1985; Paul et al., Am J Vet Res 48:684-685, 1987; Rohrer and Evans, Vet Res Commun 14:156-165, 1990). Our study yielded similar results. In our study population, the frequency of the homozygous mutant genotype was 35%. Interestingly, in a separate sample of Collies from Michigan, all dogs carried at least one mutant allele. From the pedigrees available, 8/40 from this sample and 15/15 from the Michigan sample, none of the Washington/Idaho dogs were related to the Michigan dogs within the four most recent generations. Collectively, these results suggest that the MDR1 mutation associated with ivermectin sensitivity is widely dispersed in the Collie population.

Sporadic descriptions of ivermectin sensitivity have been reported in a few other breeds including Shetland sheepdogs, Australian shepherds, and Old English sheepdogs (Hadrick et al., JAVMA 206:1147-1150, 1995; Paradis, Compend Cont Ed Pract Vet 20:193-200, 1998; Hsu et al., Compend Cont Ed Pract Vet 11:584-588, 1989). Whether or not these breeds share the same MDR1 mutation as Collies is unknown. In people, several different MDR1 mutations have been described, so it is reasonable to assume that other breeds may not share the same MDR1 genotype as do Collies (Cascorbi et al., Clin Pharmacol Ther 69:169-174, 2001; Kerb et al., Pharmacogenomics 1:51-64, 2001).

Determination of the genotype of Collies is important clinically for several reasons. First, ivermectin is not the only clinically relevant substrate for P-gp that can cause neurotoxicity. The over-the-counter antidiarrheal agent loperamide has been reported to cause neurotoxicity in Collies at doses routinely used in other breeds (Hugnet et al., Vet Hum Toxicol 38:31-33, 1996). Loperamide, like ivermectin, is generally excluded from entering brain tissue in high concentrations by the actions of P-gp. In affected Collies, loperamide achieves high concentrations in brain tissue causing neurologic toxicity. In support of this fact, one of the Collies in the present study was treated with an appropriate dose of loperamide as a puppy and developed severe (nearly fatal) neurologic toxicity. The dog tested homozygous for the mutant allele. Other drugs that are substrates for P-gp and that can cause neurotoxicity in affected Collies include vincristine, vinblastine, ondansetron, and potentially moxidectin.

There are other, non-neurologic, implications for Collies with the MDR1 mutation described. P-glycoprotein is normally also expressed at the luminal border of the intestinal tract (Liu and Hu, Clin Chem Lab Med 38:877-881, 2000), where it functions as an “anti-absorption” mechanism for a number of drugs, including digoxin, cyclosporin A, dexamethasone, antiviral drugs and others (Wacher et al., Advanced Drug Delivery Rev 46:89-102, 2001). In affected Collies, oral bioavailability of these drugs is likely to be greater than in unaffected dogs. This would result in higher plasma concentrations and a higher likelihood of adverse drug reactions in affected Collies.

It is likely that a high percentage of Collies presented to veterinarians for treatment are affected by the MDR1 mutation described in this report. It is important that veterinarians consider this factor when selecting pharmacological therapy for Collies. Furthermore, an adverse drug reaction involving neurologic toxicity should be considered for Collies exhibiting abnormal CNS signs.

Example 3 Other mdr1 Truncations

With the provision herein of the correlation between a canine mdr1 gene truncation and ivermectin sensitivity, the isolation and identification of additional mdr1 truncations, and similar truncations in other canine species, is enabled. Conventional methods for the identification of genetic polymorphisms in a population can be used to identify such additional polymorphisms.

For instance, existing populations (e.g. Collie or other populations) are assessed for ivermectin sensitivity (or sensitivity to other drugs that interact with P-gp), and a subset of individuals within the population (such as those subjects known to be prone to neurotoxicosis, or related individuals) are genotyped as relates to an mdr1 sequence. These mdr1 sequences are then compared to a reference mdr1 sequence, such as the frame-shift truncation allele described herein, to determine the presence of one or more variant nucleotide positions. After variant nucleotides are identified, statistical analysis of the population can be used to determine whether these variants are correlated with sensitivity to ivermectin or other drug treatment.

Alternatively, the P-gp protein itself can be analyzed in such subjects, to determine the presence and/or level and/or size of the protein.

Example 4 Clinical Uses of mdr1 Polymorphisms

To perform a diagnostic test for the presence or absence of a truncation mutation (e.g., a deletion, frameshift, point mutation, or other change that results in a truncated protein product) in an mdr1 sequence of an individual, a suitable genomic DNA-containing sample from a subject is obtained and the DNA extracted using conventional techniques. Most typically, a blood sample, a buccal swab, a hair follicle preparation, or a nasal aspirate is used as a source of cells to provide the DNA sample. The extracted DNA is then subjected to amplification, for example according to standard procedures. The allele of the truncation mutation is determined by conventional methods including manual and automated fluorescent DNA sequencing, primer extension methods (Nikiforov, et al., Nucl. Acids Res. 22:4167-4175, 1994), oligonucleotide ligation assay (OLA) (Nickerson et al., Proc. Natl. Acad. Sci. USA 87:8923-8927, 1990), allele-specific PCR methods (Rust et al., Nucl. Acids Res. 6:3623-3629, 1993), RNase mismatch cleavage, single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), Taq-Man, oligonucleotide hybridization, and the like. Also, see the following U.S. Patents for descriptions of methods or applications of polymorphism analysis to disease prediction and/or diagnosis: U.S. Pat. Nos. 4,666,828; 4,801,531; 5,110,920; 5,268,267; and 5,387,506.

The markers of ivermectin sensitivity disclosed herein can be utilized for the detection of, and differentiation of, individuals who are homozygous and heterozygous for the truncation mutation polymorphism(s). The value of identifying individuals who carry a sensitive allele of mdr1 (i.e., individuals who are heterozygous or homozygous for an allele that contains a “sensitive” mdr1 polymorphism, such as the truncation described herein) is that therapy for these individuals can then be initiated or customized (e.g., through avoiding ivermectin or other drugs usually kept from crossing the blood-brain barrier by P-gp) to reduce the occurrence of neurotoxicity in these individuals. Likewise, the presence of the allele will assist breeders in breeding programs, either to avoid introducing a sensitive allele into a breeding population, or by selectively avoiding animals carrying such an allele. Information regarding an animal's mdr1 allele status (sensitive, resistant, or heterozygous) could for instance be tested early in the life of the individual, and included on a license, medical record, pedigree, and so forth.

Example 5 Polymorphism Gene Probes and Markers

Sequences surrounding and overlapping truncation polymorphisms in the mdr1 gene can be useful for a number of gene mapping, targeting, and detection procedures. For example, genetic probes can be readily prepared for hybridization and detection of the described truncation polymorphism. Such probe sequences may be greater than about 12 or more oligonucleotides in length and possess sufficient complementarity to distinguish between a wild-type sequence and a sequence in which four nucleotides (e.g. nucleotides corresponding to positions 294-297 of SEQ ID NO: 1) have been lost.

Similarly, sequences surrounding and overlapping the specifically disclosed truncation polymorphism (or other polymorphisms found in accordance with the present teachings) can be utilized in allele-specific hybridization procedures. A similar approach can be adopted to detect other mdr1 polymorphisms, such as truncations.

Sequence surrounding and overlapping a mdr1 polymorphism, or any portion or subset thereof that allows one to identify the polymorphism, are highly useful. Thus, another embodiment provides a genetic marker predictive of the herein-disclosed frame-shift truncation polymorphism of mdr1, comprising a partial sequence of the canine genome including at least about 10 contiguous nucleotide residues including residues 294-297 of SEQ ID NO: 1, or specifically not including these four residues but still including the surrounding residues (in other words, specific for a deletion mutant in these four residues). Examples of such oligonucleotides include the following nucleotide sequence: AAACATGACAGATAGCTTTGCAAAT (corresponding to residues 284-309 of SEQ ID NO: 1), and sequences complementary therewith, wherein the underlined four nucleotides can be left out to create an oligonucleotide specific for the disclosed gene truncation mutation.

Example 6 Detecting mdr1 Mutations

The truncation mutation at nucleotide residue 294-297 of SEQ ID NO: 1 of canine mdr1 (the first position of which encodes amino acid residue 75 of P-gp, SEQ ID NO: 2) can be detected by a variety of techniques. These techniques include allele-specific oligonucleotide hybridization (ASOH) (Stoneking et al., Am. J. Hum. Genet. 48:370-382, 1991), which involves hybridization of oligonucleotide probes to the sequence, stringent washing, and signal detection. Other applicable methods include techniques that incorporate more robust scoring of hybridization. Examples of these procedures include the ligation chain reaction (ASOH plus selective ligation and amplification), as disclosed in Wu and Wallace (Genomics 4:560-569, 1989); mini-sequencing (ASOH plus a single base extension) as discussed in Syvanen (Meth. Mol. Biol. 98:291-298, 1998); and the use of DNA chips (miniaturized ASOH with multiple oligonucleotide arrays) as disclosed in Lipshutz et al. (Biotechniques 19:442-447, 1995). Alternatively, ASOH with single- or dual-labeled probes can be merged with PCR, as in the 5′-exonuclease assay (Heid et al., Genome Res. 6:986-994, 1996), or with molecular beacons (as in Tyagi and Kramer, Nat. Biotechnol. 14:303-308, 1996).

Another technique is dynamic allele-specific hybridization (DASH), which involves dynamic heating and coincident monitoring of DNA denaturation, as disclosed by Howell et al. (Nat. Biotech. 17:87-88, 1999). A target sequence is amplified (e.g., by PCR) using one biotinylated primer. The biotinylated product strand is bound to a streptavidin-coated microtiter plate well (or other suitable surface), and the non-biotinylated strand is rinsed away with alkali wash solution. An oligonucleotide probe, specific for one allele (e.g., the wild-type allele), is hybridized to the target at low temperature. This probe forms a duplex DNA region that interacts with a double strand-specific intercalating dye. When subsequently excited, the dye emits fluorescence proportional to the amount of double-stranded DNA (probe-target duplex) present. The sample is then steadily heated while fluorescence is continually monitored. A rapid fall in fluorescence indicates the denaturing temperature of the probe-target duplex. Using this technique, a single-base mismatch between the probe and target results in a significant lowering of melting temperature (T_(m)) that can be readily detected.

A variety of other techniques can be used to detect the polymorphisms in DNA. Merely by way of example, see U.S. Pat. Nos. 4,666,828; 4,801,531; 5,110,920; 5,268,267; 5,387,506; 5,691,153; 5,698,339; 5,736,330; 5,834,200; 5,922,542; and 5,998,137 for such methods.

Example 7 Expression of P-gp

The expression and purification of proteins, such as the P-gp, can be performed using standard laboratory techniques. After expression, purified P-gp may be used for functional analyses, antibody production, diagnostics, and patient therapy. Furthermore, the DNA sequence of the mdr1 cDNA can be manipulated in studies to understand the expression of the gene and the function of its product. Mutant forms of the canine mdr1 gene may be isolated based upon information contained herein, and may be studied in order to detect alteration in expression patterns in terms of relative quantities, tissue specificity, molecular weight, stability, and functional properties of the encoded mutant P-gp protein. Partial or full-length cDNA sequences, which encode for the subject protein, may be ligated into bacterial expression vectors. Methods for expressing large amounts of protein from a cloned gene introduced into Escherichia coli (E. coli) may be utilized for the purification, localization and functional analysis of proteins. For example, fusion proteins consisting of amino terminal peptides encoded by a portion of the E. coli lacZ or trpE gene linked to P-gp proteins may be used to prepare polyclonal and monoclonal antibodies against these proteins. Thereafter, these antibodies may be used to purify proteins by immunoaffinity chromatography, in diagnostic assays to quantitate the levels of protein and to localize proteins in tissues and individual cells by immunofluorescence.

Intact native protein may also be produced in E. coli in large amounts for functional studies. Methods and plasmid vectors for producing fusion proteins and intact native proteins in bacteria are described in Sambrook et al. (In Molecular Cloning: A Laboratory Manual, Ch. 17, CSHL, New York, 1989). Such fusion proteins may be made in large amounts, are easy to purify, and can be used to elicit antibody response. Native proteins can be produced in bacteria by placing a strong, regulated promoter and an efficient ribosome-binding site upstream of the cloned gene. If low levels of protein are produced, additional steps may be taken to increase protein production; if high levels of protein are produced, purification is relatively easy. Suitable methods are presented in Sambrook et al. (In Molecular Cloning: A Laboratory Manual, CSHL, New York, 1989) and are well known in the art. Often, proteins expressed at high levels are found in insoluble inclusion bodies. Methods for extracting proteins from these aggregates are described by Sambrook et al. (In Molecular Cloning: A Laboratory Manual, Ch. 17, CSHL, New York, 1989). Vector systems suitable for the expression of lacZ fusion genes include the pUR series of vectors (Ruther and Muller-Hill, EMBO J. 2:1791, 1983), pEX1-3 (Stanley and Luzio, EMBO J. 3:1429, 1984) and pMR100 (Gray et al., Proc. Natl. Acad. Sci. USA 79:6598, 1982). Vectors suitable for the production of intact native proteins include pKC30 (Shimatake and Rosenberg, Nature 292:128, 1981), pKK177-3 (Amann and Brosius, Gene 40:183, 1985) and pET-3 (Studiar and Moffatt, J. Mol. Biol. 189:113, 1986). P-gp fusion proteins may be isolated from protein gels, lyophilized, ground into a powder and used as an antigen. The DNA sequence can also be transferred from its existing context to other cloning vehicles, such as other plasmids, bacteriophages, cosmids, animal viruses and yeast artificial chromosomes (YACs) (Burke et al., Science 236:806-812, 1987). These vectors may then be introduced into a variety of hosts including somatic cells, and simple or complex organisms, such as bacteria, fungi (Timberlake and Marshall, Science 244:1313-1317, 1989), invertebrates, plants (Gasser and Fraley, Science 244:1293, 1989), and animals (Pursel et al., Science 244:1281-1288, 1989), which cell or organisms are rendered transgenic by the introduction of the heterologous mdr1 cDNA.

For expression in mammalian cells, the cDNA sequence may be ligated to heterologous promoters, such as the simian virus (SV) 40 promoter in the pSV2 vector (Mulligan and Berg, Proc. Natl. Acad. Sci. USA 78:2072-2076, 1981), and introduced into cells, such as monkey COS-1 cells (Gluzman, Cell 23:175-182, 1981), to achieve transient or long-term expression. The stable integration of the chimeric gene construct may be maintained in mammalian cells by biochemical selection, such as neomycin (Southern and Berg, J. Mol. Appl. Genet. 1:327-341, 1982) and mycophenolic acid (Mulligan and Berg, Proc. Natl. Acad. Sci. USA 78:2072-2076, 1981).

DNA sequences can be manipulated with standard procedures such as restriction enzyme digestion, fill-in with DNA polymerase, deletion by exonuclease, extension by terminal deoxynucleotide transferase, ligation of synthetic or cloned DNA sequences, site-directed sequence-alteration via single-stranded bacteriophage intermediate or with the use of specific oligonucleotides in combination with PCR.

The cDNA sequence (or portions derived from it) or a mini gene (a cDNA with an intron and its own promoter) may be introduced into eukaryotic expression vectors by conventional techniques. These vectors are designed to permit the transcription of the cDNA in eukaryotic cells by providing regulatory sequences that initiate and enhance the transcription of the cDNA and ensure its proper splicing and polyadenylation. Vectors containing the promoter and enhancer regions of the SV40 or long terminal repeat (LTR) of the Rous Sarcoma virus and polyadenylation and splicing signal from SV40 are readily available (Mulligan et al., Proc. Natl. Acad. Sci. USA 78:1078-2076, 1981; Gorman et al., Proc. Natl. Acad. Sci. USA 78:6777-6781, 1982). The level of expression of the cDNA can be manipulated with this type of vector, either by using promoters that have different activities. For example, the baculovirus pAC373 can express cDNAs at high levels in S. frugiperda cells (Summers and Smith, In Genetically Altered Viruses and the Environment, Fields et al. (Eds.) 22:319-328, CSHL Press, Cold Spring Harbor, N.Y., 1985) or by using vectors that contain promoters amenable to modulation, for example, the glucocorticoid-responsive promoter from the mouse mammary tumor virus (Lee et al., Nature 294:228, 1982). The expression of the cDNA can be monitored in the recipient cells 24 to 72 hours after introduction (transient expression).

In addition, some vectors contain selectable markers such as the gpt (Mulligan and Berg, Proc. Natl. Acad. Sci. USA 78:2072-2076, 1981) or neo (Southern and Berg, J. Mol. Appl. Genet. 1:327-341, 1982) bacterial genes. These selectable markers permit selection of transfected cells that exhibit stable, long-term expression of the vectors (and therefore the cDNA). The vectors can be maintained in the cells as episomal, freely replicating entities by using regulatory elements of viruses such as papilloma (Sarver et al., Mol. Cell Biol. 1:486, 1981) or Epstein-Barr (Sugden et al., Mol. Cell Biol. 5:410, 1985). Alternatively, one also can produce cell lines that have integrated the vector into genomic DNA. Both of these types of cell lines produce the gene product on a continuous basis. One can also produce cell lines that have amplified the number of copies of the vector (and therefore of the cDNA as well) to create cell lines that can produce high levels of the gene product (Alt et al., J. Biol. Chem. 253:1357, 1978).

The transfer of DNA into eukaryotic, in particular human or other mammalian cells, is now a conventional technique. The vectors are introduced into the recipient cells as pure DNA (transfection) by, for example, precipitation with calcium phosphate (Graham and van der Eb, Virology 52:456-467, 1973) or strontium phosphate (Brash et al., Mol. Cell Biol. 7:2013, 1987), electroporation (Neumann et al., EMBO J 1:841, 1982), lipofection (Felgner et al., Proc. Natl. Acad. Sci USA 84:7413, 1987), DEAE dextran (McCuthan et al., J. Natl. Cancer Inst. 41:351, 1968), microinjection (Mueller et al., Cell 15:579, 1978), protoplast fusion (Schafner, Proc. Natl. Acad. Sci. USA 77:2163-2167, 1980), or pellet guns (Klein et al., Nature 327:70, 1987). Alternatively, the cDNA, or fragments thereof, can be introduced by infection with virus vectors. Systems are developed that use, for example, retroviruses (Bernstein et al., Gen. Engr. 7:235, 1985), adenoviruses (Ahmad et al., J. Virol. 57:267, 1986), or Herpes virus (Spaete et al., Cell 30:295, 1982). P-gp encoding sequences also can be delivered to target cells in vitro via non-infectious systems, for instance liposomes.

These eukaryotic expression systems can be used for studies of P-gp encoding nucleic acids and mutant forms of these molecules, the P-gp protein and mutant forms of this protein.

Using the above techniques, the expression vectors containing the mdr1 gene sequence or cDNA, or fragments or variants or mutants thereof, can be introduced into canine cells, mammalian cells from other species, or non-mammalian cells as desired. The choice of cell is determined by the purpose of the introduction. For example, monkey COS cells (Gluzman, Cell 23:175-182, 1981) that produce high levels of the SV40 T antigen and permit the replication of vectors containing the SV40 origin of replication may be used. Similarly, Chinese hamster ovary (CHO), mouse NIH 3T3 fibroblasts or canine fibroblasts or lymphoblasts may be used.

This disclosure thus encompasses recombinant vectors that comprise all or part of the mdr1 gene or cDNA sequences, for expression in a suitable host. The mdr1 DNA is operatively linked in the vector to an expression control sequence in the recombinant DNA molecule so that the P-gp polypeptide can be expressed. The expression control sequence may be selected from the group consisting of sequences that control the expression of genes of prokaryotic or eukaryotic cells and their viruses and combinations thereof. The expression control sequence may be specifically selected from the group consisting of the lac system, the trp system, the tac system, the trc system, major operator and promoter regions of phage lambda, the control region of fd coat protein, the early and late promoters of SV40, promoters derived from polyoma, adenovirus, retrovirus, baculovirus and simian virus, the promoter for 3-phosphoglycerate kinase, the promoters of yeast acid phosphatase, the promoter of the yeast alpha-mating factors and combinations thereof.

The host cell, which may be transfected with a vector described herein, may be selected from the group consisting of E. coli, Pseudomonas, Bacillus subtilis, Bacillus stearothermophilus or other bacilli; other bacteria; yeast; fungi; insect; mouse or other animal; or plant hosts; or human or canine tissue cells.

It is appreciated that, for mutant or variant mdr1 DNA sequences, similar systems are employed to express and produce the mutant product. In addition, fragments of the P-gp protein can be expressed essentially as detailed above. Such fragments include individual P-gp protein domains or sub-domains, as well as shorter fragments such as peptides. P-gp protein fragments having therapeutic properties may be expressed in this manner also.

Example 8 Production of P-gp Protein Specific Binding Agents

Monoclonal or polyclonal antibodies may be produced to either the normal P-gp or mutant forms (e.g., truncations) of this protein. Optimally, antibodies raised against these proteins or peptides would specifically detect the protein or peptide with which the antibodies are generated. That is, an antibody generated to the P-gp or a fragment thereof would recognize and bind the P-gp and would not substantially recognize or bind to other proteins found in human cells.

The determination that an antibody specifically detects P-gp is made by any one of a number of standard immunoassay methods; for instance, the Western blotting technique (Sambrook et al., In Molecular Cloning: A Laboratory Manual, CSHL, New York, 1989). To determine that a given antibody preparation (such as one produced in a mouse) specifically detects P-gp by Western blotting, total cellular protein is extracted from human cells (for example, lymphocytes) and electrophoresed on a sodium dodecyl sulfate-polyacrylamide gel. The proteins are then transferred to a membrane (for example, nitrocellulose) by Western blotting, and the antibody preparation is incubated with the membrane. After washing the membrane to remove non-specifically bound antibodies, the presence of specifically bound antibodies is detected by the use of an anti-mouse antibody conjugated to an enzyme such as alkaline phosphatase. Application of an alkaline phosphatase substrate 5-bromo4-chloro-3-indolyl phosphate/nitro blue tetrazolium results in the production of a dense blue compound by immunolocalized alkaline phosphatase. Antibodies that specifically detect P-gp will, by this technique, be shown to bind to P-gp band (which will be localized at a given position on the gel determined by its molecular weight). Non-specific binding of the antibody to other proteins may occur and may be detectable as a weak signal on the Western blot. The non-specific nature of this binding will be recognized by one skilled in the art by the weak signal obtained on the Western blot relative to the strong primary signal arising from the specific antibody-P-gp binding.

Substantially pure P-gp or protein fragments (peptides) suitable for use as an immunogen may be isolated from transfected or transformed cells as described above. Concentration of protein or peptide in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms per milliliter. Monoclonal or polyclonal antibody to the protein can then be prepared using one of the following techniques.

A. Monoclonal Antibody Production by Hybridoma Fusion

Monoclonal antibody to epitopes of P-gp, or specifically to the truncation protein identified and isolated as described can be prepared from murine hybridomas according to the classical method of Kohler and Milstein (Nature 256:495-497, 1975) or derivative methods thereof. Briefly, a mouse is repetitively inoculated with a few micrograms of the selected protein over a period of a few weeks. The mouse is then sacrificed, and the antibody-producing cells of the spleen isolated. The spleen cells are fused by means of polyethylene glycol with mouse myeloma cells, and the excess un-fused cells destroyed by growth of the system on selective media comprising aminopterin (HAT media). The successfully fused cells are diluted and aliquots of the dilution placed in wells of a microtiter plate where growth of the culture is continued. Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall (Meth. Enzymol. 70:419-439, 1980), and derivative methods thereof. Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are described in Harlow and Lane (Antibodies, A Laboratory Manual, CSHL, New York, 1988).

B. Polyclonal Antibody Production by Immunization

Polyclonal antiserum containing antibodies to heterogeneous epitopes of a single protein can be prepared by immunizing suitable animals with the expressed protein (Example 7), which can be unmodified or modified to enhance immunogenicity. Effective polyclonal antibody production is affected by many factors related both to the antigen and the host species. For example, small molecules tend to be less immunogenic than others and may require the use of carriers and adjuvant. Also, host animals vary in response to site of inoculations and dose, with either inadequate or excessive doses of antigen resulting in low titer antisera. Small doses (ng level) of antigen administered at multiple intradermal sites appear to be most reliable. An effective immunization protocol for rabbits can be found in Vaitukaitis et al. (J. Clin. Endocrinol. Metab. 33:988-991, 1971).

Booster injections can be given at regular intervals, and antiserum harvested when antibody titer thereof, as determined semi-quantitatively, for example, by double immunodiffusion in agar against known concentrations of the antigen, begins to fall. See, for example, Ouchterlony et al. (In Handbook of Experimental Immunology, Wier, D. (ed.) chapter 19. Blackwell, 1973). Plateau concentration of antibody is usually in the range of about 0.1 to 0.2 mg/ml of serum (about 12 μM). Affinity of the antisera for the antigen is determined by preparing competitive binding curves, as described, for example, by Fisher (Manual of Clinical Immunology, Ch. 42, 1980).

C. Antibodies Raised Against Synthetic Peptides

A third approach to raising antibodies against P-gp or peptides is to use one or more synthetic peptides synthesized on a commercially available peptide synthesizer based upon the predicted amino acid sequence of P-gp or peptide. Polyclonal antibodies can be generated by injecting these peptides into, for instance, rabbits.

D. Antibodies Raised by Injection of P-gp Encoding Sequence

Antibodies may be raised against P-gp proteins and peptides by subcutaneous injection of a DNA vector that expresses the desired protein or peptide, or a fragment thereof, into laboratory animals, such as mice. Delivery of the recombinant vector into the animals may be achieved using a hand-held form of the Biolistic system (Sanford et al., Particulate Sci. Technol. 5:27-37, 1987) as described by Tang et al. (Nature 356:152-154, 1992). Expression vectors suitable for this purpose may include those that express the P-gp encoding sequence (mdr1 gene or cDNA, for instance) under the transcriptional control of either the human β-actin promoter or the cytomegalovirus (CMV) promoter.

Antibody preparations prepared according to these protocols are useful in quantitative immunoassays which determine concentrations of antigen-bearing substances in biological samples; they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample; or for immunolocalization of P-gp.

For administration to specific animal subjects (such as human or canine individuals), antibodies, e.g., P-gp specific monoclonal antibodies, can be adapted to be more effective in the target organism by methods known in the art. By way of example, antibodies with a desired binding specificity can be commercially humanized (Scotgene, Scotland, UK; Oxford Molecular, Palo Alto, Calif.).

Example 9 Protein-Based Detection

An alternative method of detecting sensitivity to ivermectin and related drugs (those that are kept from crossing the blood-brain barrier by P-gp) is to examine the level or molecular weight (apparent size, e.g., on after SDS-PAGE with or without immunodetection) of P-gp in the cells of an individual. These diagnostic tools would be useful for detecting reduced levels of P-gp that result from, for example, mutations in the promoter regions of the mdr1 gene or mutations within the coding region of the gene that produced truncated, non-functional or unstable polypeptides, as well as from deletions of a portion of or the entire mdr1 gene.

Localization and/or coordinated mdr1 expression (temporally or spatially) can also be examined using known techniques, such as isolation and comparison of P-gp from cell or tissue specific, or time specific, samples. The determination of reduced or increased P-gp levels, in comparison to such expression in a control cell (e.g., normal, as in taken from an individual not exhibiting sensitivity to ivermectin or another neurotoxin), would be an alternative or supplemental approach to the direct determination of mdr1 gene mutation (e.g., truncation mutation) status by the methods outlined above and equivalents.

The availability of antibodies specific to P-gp will facilitate the detection, measurement (e.g., molecular weight determination) and quantitation of cellular P-gp by one of a number of immunoassay methods which are well known in the art and are presented in Harlow and Lane (Antibodies, A Laboratory Manual, CSHL, New York, 1988). Methods of constructing such antibodies are discussed above, in Example 8.

Any standard immunoassay format (e.g., ELISA, Western blot, or RIA assay) can be used to measure P-gp polypeptide or protein levels; comparison is to wild-type (normal) P-gp, and an alteration in P-gp polypeptide may be indicative of an abnormal biological condition regarding resistance to potential neurotoxins, such as ivermectin. Immunohistochemical techniques may also be utilized for P-gp polypeptide or protein detection. For example, a tissue sample may be obtained from a subject, and a section stained for the presence of P-gp using a P-gp specific binding agent (e.g., anti-P-gp antibody) and any standard detection system (e.g., one which includes a secondary antibody conjugated to horseradish peroxidase). General guidance regarding such techniques can be found in, e.g., Bancroft and Stevens (Theory and Practice of Histological Techniques, Churchill Livingstone, 1982) and Ausubel et al. (Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1998).

For the purposes of quantifying or determining the estimated molecular weight of P-gp, a biological sample of the subject (which can be any animal, for instance a dog or a human), which sample includes cellular proteins, is required. Such a biological sample may be obtained from body cells, such as those present in peripheral blood, urine, saliva, tissue biopsy, amniocentesis samples, surgical specimens and autopsy material. Quantitation and/or measurement of P-gp can be achieved by immunoassay and compared to level and apparent size of the protein found in control cells (e.g., healthy, as in from an individual known not to have ivermectin sensitivity). A significant (e.g., 10% or greater) reduction in the amount of P-gp in the cells of a test subject compared to the amount of P-gp found in normal cells, or a substantial reduction in the apparent molecular weight of the P-gp (e.g., as would be apparent with a truncation mutation) could be taken as an indication that the subject may have deletions or mutations in the mdr1 gene. Deletion and/or mutation of or within the mdr1-encoding sequence, and substantial under-expression of P-gp, may be indicative of altered sensitivity to ivermectin and other drugs that are usually kept from crossing the blood-brain barrier by P-gp.

Merely by way of example, canine P-gp can be analyzed as described in Mealey et al., Cancer Letters 126:187-192, 1998. For instance, immunoblotting has been carried out using the following procedure:

Cells were harvested by trypsinization, washed with DPBS and solubilized in tumor solubilization buffer (TSB, 50 mM Tris-HCl (pH 6.8), 50 mM KCl, 5 mM EGTA, 5 mM MgCl₂, 2% CHAPS, 0.1 mM leupeptin, 0.2 mM phenylmethyl-sulfonylfluoride and 10 mM dithiothreitol). Insoluble complexes were cleared by a 5-minute spin (1500 revolutions/minute) and the soluble protein was collected for quantitation using a modified Lowry technique (Lowry, J. Biol. Chem. 193:265-275, 1951).

Protein samples were separated by SDS-PAGE and electroblotted onto an Immobilon-P™ membrane (Millipore, Bedford, Mass.). Membranes were washed with blotto buffer (50 mM Tris-HCl, 2 mM CaCl₂, 80 mM NaCl, 5% non-fat dry milk, 0.2% Nonidet P-40 and 0.03% sodium azide) for one hour at 25° C. and then incubated (25° C. for 16 hours) with a murine anti-human P-glycoprotein monoclonal antibody (C219; Signet, Dedham, Mass.). Actin was subsequently detected using a monoclonal anti-actin antibody (ICN Immunobiologicals, Costa Mesa, Calif.). Membranes were washed in fresh blotto (non-fat milk) buffer and incubated with the appropriate alkaline phosphatase-labeled secondary antibody. Membranes were washed with buffer A (50 mM Tris-HCl, 2 mM CaCl₂ and 80 mM NaCl) and developed using nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate with an alkaline-phosphatase conjugate substrate kit (BioRad, Hercules, Calif.). The color reaction was terminated by washing in distilled water. The resulting bands were scanned with a Visage 110 camera-based densitometer (Bio-Image, Ann Arbor, Minn.) and analyzed using whole band software. Integrated intensity signals for P-glycoprotein can be normalized to those of a protein the level of which is not expected to change under the experimental conditions.

Example 10 Differentiation of Individuals Homozygous Versus Heterozygous for the Polymorphism(s)

As will be appreciated, the oligonucleotide ligation assay (OLA), as described at Nickerson et al. (Proc. Natl. Acad. Sci. USA 87:8923-8927, 1990), allows the differentiation between individuals who are homozygous versus heterozygous for the herein-described frame-shift truncation mutation in mdr1. This feature allows one to rapidly and easily determine whether an individual is homozygous for at least a neurotoxin sensitivity-linked polymorphism, which condition can result in neurotoxicosis and possible death when an individual is administered an otherwise safe drug dosage. Alternatively, OLA can be used to determine whether a subject is homozygous for either of these polymorphisms.

As an example of the OLA assay, when carried out in microtiter plates, one well is used for the determination of the presence of the mdr1 allele that contains the herein-described frame-shift truncation mutation, and a second well is used for the determination of the presence of the mdr1 wild-type allele. Thus, the results for an individual who is heterozygous for the polymorphism will show a signal in each of the “truncated” and wild-type wells, and an individual who is homozygous for one allele or the other will show a signal only in the corresponding well.

Likewise, truncation itself can be used to detect heterogeneity in the P-gp protein. Because truncation leads to production of a shorter (and therefore “lighter”) protein product, Western analysis can be used to distinguish between heterozygous and homozygous individuals, as well as between homozygous truncated (and therefore sensitive) and wild-type (resistant) individuals.

Example 11 Kits

Kits are provided which contain the necessary reagents for determining the presence or absence of polymorphism(s) in a P-gp-encoding sequence, such as probes or primers specific for the mdr1 gene. Such kits can be used with the methods described herein to determine whether an individual is likely to be sensitive to ivermectin and other drugs that are usually kept from crossing the blood-brain barrier by P-gp (such as those listed in Table II).

The provided kits may also include written instructions. The instructions can provide calibration curves or charts to compare with the determined (e.g., experimentally measured) values.

Kits are also provided to determine altered (e.g., lowered) expression of mRNA (i.e., containing probes) or P-gp protein (i.e., containing antibodies or other P-gp-specific binding agents), as well as truncated P-gp.

A. Kits for Detecting mdr1 Nucleic Acid Mutations

The oligonucleotide probes and primers disclosed herein can be supplied in the form of a kit, for use in detection of ivermectin sensitivity in a subject. In such a kit, an appropriate amount of one or more of the oligonucleotides is provided in one or more containers. The oligonucleotides may be provided suspended in an aqueous or other solution, or as a freeze-dried or lyophilized powder, for instance. The container(s) in which the oligonucleotide(s) are supplied can be any conventional container that is capable of holding the supplied form, for instance, microfuge tubes, ampoules, or bottles. In some applications, pairs of primers may be provided in pre-measured single use amounts in individual, typically disposable, tubes or equivalent containers. With such an arrangement, the sample to be tested for the presence of an mdr1 polymorphism can be added to the individual tubes and amplification or other laboratory manipulation carried out directly.

The amount of each oligonucleotide supplied in the kit can be any appropriate amount, depending for instance on the market to which the product is directed. For instance, if the kit is adapted for research or clinical use, the amount of each oligonucleotide primer provided would likely be an amount sufficient to prime several in vitro nucleic acid amplification reactions. Those of ordinary skill in the art know the amount of oligonucleotide primer that is appropriate for use in a single amplification reaction. General guidelines may for instance be found in Innis et al. (PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc., San Diego, Calif., 1990), Sambrook et al. (In Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., 1989), and Ausubel et al. (In Current Protocols in Molecular Biology, Greene Publ. Assoc. and Wiley-Intersciences, 1992).

A kit may include more than two primers, in order to facilitate the in vitro amplification of mdr1 sequences, for instance the mdr1 gene or the 5′- or 3′-flanking region thereof.

In some embodiments, kits may also include the reagents necessary to carry out nucleotide amplification reactions, including, for instance, DNA sample-preparation reagents, appropriate buffers (e.g., polymerase buffer), salts (e.g., magnesium chloride), and deoxyribonucleotides (dNTPs).

Kits may include either labeled or unlabeled oligonucleotide probes for use in detection of mdr1 polymorphism(s). In certain embodiments, these probes will be specific for a potential polymorphism that may be present in the target sequence. The appropriate sequences for such a probe will be any sequence that includes all or part of the identified polymorphic site, particularly nucleotide positions 294 through 297 of the canine mdr1 gene, such that the sequence the probe is complementary to the truncation polymorphic site and a portion of the surrounding mdr1 sequence. An oligonucleotide including the sequence AAACATGACAGATAGCTTTGCAAAT (corresponding to residues 284-309 of SEQ ID NO: 1) exemplifies such a sequence, and a probe useful for disclosed methods could comprise this sequence. Alternatively, an example of a probe specific for detecting the ivermectin sensitivity allele of mdr1 may include the following sequence: AAACATGACAGCTTTGCAAAT (also corresponding to residues 284-309 of SEQ ID NO: 1, but with residues 294-297 removed).

It also may be advantageous to provide in the kit one or more control sequences for use in the amplification reactions. The design of appropriate positive and negative control sequences is well known to one of ordinary skill in the appropriate art.

B. Kits for Detection of mdr1 mRNA

Kits similar to those disclosed above for the detection of mdr1 polymorphisms directly can be used to detect mdr1 mRNA expression, such as over- or under-expression or expression of a truncated form. Such kits include an appropriate amount of one or more oligonucleotide primers for use in, for instance, reverse transcription nucleic acid amplification reactions (e.g., RT-PCR), similarly to those oligonucleotides described above with art-obvious modifications for use with RNA amplification.

In some embodiments, kits for detection of altered expression of mdr1 mRNA may also include some or all of the reagents necessary to carry out RT-PCR or other in vitro amplification reactions, for instance, RNA sample preparation reagents (including e.g., an RNase inhibitor), appropriate buffers (e.g., polymerase buffer), salts (e.g., magnesium chloride), and deoxyribonucleotides (dNTPs). Written instructions also may be included.

Such kits may in addition include either labeled or unlabeled oligonucleotide probe(s) for use in detection of the in vitro amplified target sequences. The appropriate sequences for such a probe will be any sequence that falls between the annealing sites of the two provided oligonucleotide primers, such that the sequence the probe is complementary to is amplified during the in vitro amplification reaction. In certain embodiments, these probes will be specific for a potential polymorphism that may be present in the amplified target sequences.

It also may be advantageous to provide in the kit one or more control sequences for use in the RT-PCR reactions. The design of appropriate positive and negative control sequences is well known to one of ordinary skill in the appropriate art.

Alternatively, kits may be provided with the necessary reagents to carry out quantitative or semi-quantitative Northern analysis of mdr1 mRNA. Such kits include, for instance, at least one mdr1-specific oligonucleotide for use as a probe. This oligonucleotide may be labeled in any conventional way, including with a selected radioactive isotope, enzyme substrate, co-factor, ligand, chemiluminescent or fluorescent agent, hapten, or enzyme. In certain embodiments, such probes will be specific for a potential polymorphism (e.g., a truncation mutation) that may be present in the target sequences.

C. Kits For Detection of P-gp Expression

Kits for the detection of P-gp protein expression (such as over- or under-expression), and particularly changes in the apparent molecular weight of expressed P-gp, are also encompassed herein. Such kits may include at least one target-protein-specific binding agent (e.g., a polyclonal or monoclonal antibody or antibody fragment that specifically recognizes P-gp) and may include at least one control (such as a determined amount of P-gp, with a defined molecular weight or apparent size, or a sample containing a determined amount of P-gp). The P-gp-protein-specific binding agent and control may be contained in separate containers.

P-gp expression detection kits may also include a means for detecting P-gp:binding agent complexes, for instance the agent may be detectably labeled. If the binding agent is not labeled, it may be detected by second antibodies or protein A for example, which components may also be provided in some kits in one or more separate containers. Such detection techniques are known.

Additional components in specific kits may include instructions for carrying out the assay. Instructions will allow the tester to determine whether P-gp expression levels are elevated, and/or whether the expressed P-gp has an altered molecular weight compared to wild-type P-gp. Reaction vessels and auxiliary reagents such as chromogens, buffers, enzymes, etc. may also be included in the kits.

D. Kits for Detection of Homozygous Versus Heterozygous Allelism

Also provided are kits that allow differentiation between individuals who are homozygous versus heterozygous for a truncation mutation in the mdr1 gene. Certain examples of such kits provide the materials for performing oligonucleotide ligation assays (OLA), as described by Nickerson et al., Proc. Natl. Acad. Sci. USA 87:8923-8927, 1990. In specific embodiments, these kits contain one or more microtiter plate assays, designed to detect polymorphism(s) in the mdr1 sequence of a subject, as described herein.

In other examples of such kits, materials are provided for examining the size of the P-gp expressed by an individual, for instance components for carrying out a Western analysis or other immunological assay.

Additional components in some of these kits may include instructions for carrying out the assay. Instructions will allow the tester to determine whether an mdr1 truncation mutation allele is homozygous or heterozygous, either through examination of nucleic acid molecules or protein. Reaction vessels and auxiliary reagents such as chromogens, buffers, enzymes, etc. may also be included in the kits.

It may also be advantageous to provide in the kit one or more control sequences for use in the OLA or immunoassay reactions. The design of appropriate positive and negative control molecules is well known to one of ordinary skill in the appropriate art.

Example 12 Animal Model

A large number of P-gp substrates are routinely prescribed in humans, including HIV-1 protease inhibitors and many chemotherapeutic agents. Animals (e.g., Collies) possessing a polymorphism of the mdr1 gene, for instance, the truncation mutation described herein, can serve as a useful model for studying the effects of P-glycoprotein substrates on humans with mdr1 polymorphisms. In addition, these animals can serve as models for studying the effects of compounds that interact with P-gp. They are also useful to study pharmacologic inhibition of P-gp, for instance in order to identify or characterize modulators of P-gp transport activity that may be useful to increase (or decrease, or regulate) drug absorption in or distribution to one or more tissues in a subject.

Use of the animals identified herein (particularly Collies) possessing a naturally-occurring polymorphism of the mdr1 gene avoids confounding effects attributable to producing mdr1 mutations through genetic engineering, and is expected to result in better acceptance as a research model by both the research community and society.

Using methods described herein, individual animals are identified as being heterozygous or homozygous for an mdr1 truncation, and these animals are used as subjects for animal model studies. In specific examples, a drug of interest (or drug candidate or other compound or mixture thereof) is administered to Collies possessing a polymorphism of MDR-1, and the effects are monitored systemically, for instance, or in particular tissues. Routes of administration include but are not limited to oral and parenteral routes, such as intravenous (iv), intraperitoneal (ip), rectal, topical, ophthalmic, nasal, and transdermal.

Effective doses of the compound(s) of interest can be determined by one of ordinary skill in the art, and may be tailored to the specific experiments being run. In some embodiments, the compound is administered with a goal of achieving tissue concentrations that are at least as high as the IC₅₀ of the compounds(s) tested. An example of such a dosage range is 0.1 to 200 mg/kg body weight. The specific dose level and frequency of dosage for any particular subject may be varied and will depend upon a variety of factors, including the activity of the specific compound, the metabolic stability and length of action of that compound, the age, body weight, mode and time of administration, and the rate of excretion of the compound.

Systemic effects of the compound of interest can be monitored in the animal following its administration. For example, neurological symptoms linked to a drug passing across one or more cellular membranes via P-gp can include salivation, vomiting, confusion, ataxia, tremors, seizure-like activity, recumbency, non-responsiveness, and coma. Alternatively, drug or other compound levels in the blood, or biochemical changes in the gastrointestinal tract, kidneys, nervous system, liver, tumor cells, or other tissues, can be monitored.

The animal model can also be used to identify and/or characterize test compounds known to, or expected to, modulate the activity of P-gp. In examples of such methods, the animals are treated (e.g., concurrently or sequentially) with both the test compound and a compound known to be transported by P-gp (the effector molecule). The animals are then monitored to detect one or more effects caused by the effector compound, and the level of effect can be compared to animals that were not treated with the test compound (or which received a different treatment regimen). Depending on the effector molecule used, different biological characteristics of the animal, or a tissue or cell within the animal, can be monitored to determine whether (and to what extent) the test compound influences P-gp interaction with the effector. Depending on whether the test molecule increases or decreases P-gp transport of the effector, the test molecule is identified as an agonist or antagonist of P-gp activity and can be selected for further characterization.

Example 13 Cultured Cells

Cells or tissues from animals (e.g., Collies) possessing a polymorphism of the mdr1 gene, for instance, the truncation mutation described herein, also can serve as useful model systems for studying the effects of P-gp interacting molecules. In addition, cells and tissues from animals possessing a polymorphism of the mdr1 gene can serve as models for studying pharmacologic inhibition, stimulation, and/or regulation of P-gp.

In some examples of such cell-based models, cells from an animal carrying an mdr1 truncation as described herein are transformed (stably or transiently) with an mdr1 construct, for instance which comprises known (e.g., engineered) or unknown mutations (e.g., point mutations such as a naturally occurring polymorphism, for instance polymorphisms identified in human mdr1). Such cellular expression systems enable examination of the activity of the mutant mdr1 construct in a defined large mammal background.

P-gp is expressed in many tissues throughout the mammalian body, including the epithelium of the gastrointestinal tract, renal-tubular epithelium, brain capillary endothelial cells, biliary tubular epithelial cells, and at the plasma membrane in many tumor cells. In some examples, cells used for the in vitro cell system are selected from a specific tissue or cell type, so that tissue or cell specific effects of P-gp transport can be studied. In carrying out such methods, specific tissues are isolated from canines (e.g., Collies) possessing a polymorphism of the mdr1 gene, such as the truncation described herein. Though methods are widely known for isolating cells and tissues of specific types, the following procedures are provided as specific examples and can be used to isolate specific cells from canine samples:

(a) Canine intestinal epithelial cells can be isolated and cultured as described in Koop and Buchan, Gastroenterology 102: 28-34, 1992.

(b) Canine brain microvessel endothelial cells can be isolated and cultured as described in Drewes et al., Brain Research Bulletin 21: 771-776, 1988.

(c) Canine renal-tubular cells can be isolated and cultured as described in Hamada et al., Nephron. 68: 104-111, 1994.

(d) Canine hepatocytes can be isolated and cultured as described in Lu and Li, Chem. Biol. Interact. 143: 271-281, 2001, Amacher and Martin, Fundam. Appl Toxicol. 40:256-263, 1997, or Placidi et al., Drug Metab. Dispos. 25: 94-99, 1997.

(e) Neoplasms can be induced using techniques well known in the art, including but not limited to the use of chemical carcinogens, viruses, and radiation exposure. Alternatively, naturally occurring tumors can also serve as a source for cancerous cells. Tumor cells can then be cultured as described in Lehr et al., Anticancer Res. 18(6A): 4483-4488, 1998.

The cell-based model can also be used to identify and/or characterize test compounds known to, or expected to, modulate the activity of P-gp. In examples of such methods, the cells are contacted (e.g., concurrently or sequentially) with both the test compound and a compound known to be transported by P-gp (the effector molecule). The cells are then monitored to detect one or more effects caused by the effector compound, and the level of effect can be compared to animals that were not treated with the test compound (or which received a different treatment regimen). Depending on the effector molecule used, different biological characteristics of the cells can be monitored to determine whether (and to what extent) the test compound influences P-gp interaction with the effector. Depending on whether the test molecule increases or decreases P-gp transport of the effector, the test molecule is identified as an agonist or antagonist of P-gp activity and can be selected for further characterization.

Compound transport across a membrane in cultured cells can be monitored using known techniques, for instance the radio-labeling method outlined in Schinkel et al. J. Clin. Invest. 96:1698-1705, 1995. Briefly, cells are grown in complete medium including L-glutamine, penicillin, streptomycin, and FCS and seeded on microporous polycarbonate membrane filters (3.0 μM pore size, 24.5 mm diameter, Transwell™ 3414, Costar Corp., Cambridge, Md.) at a density of 2×10⁶ cells per well. Medium at either the apical or basal side of the cell layer is replaced with complete medium containing the appropriate concentration of radiolabeled drug or drug candidate and cells are incubated at 37° C. in 5% CO₂. Subsequently, 50 μl aliquots are taken from each compartment at various time intervals, for instance 1, 2, 3, and 4 hours. The appearance of radioactivity in the non-treated compartment is measured and presented as the fraction of total radioactivity added at the beginning of the experiment.

In some methods employing the provided cell systems, the level of radioactive effector compound transported into the cells is compared between cells that received treatment with a test compound (e.g., a putative or potential P-gp activity agonist or antagonist) and those that did not receive such treatment, or between cells that received different test compound treatments (for instance, as to the test compound used, the method or timing of application, the amount applied, and so forth).

Methods of monitoring compound-uptake will in some instances be influenced by the compounds being studied.

This disclosure provides a mutation in the canine (particularly collie) mdr1 gene, which results in a truncation of P-gp and leads to extreme sensitivity to ivermectin in animals homozygous for this mutant allele. The disclosure further provides methods and kits for screening for this mutation, in order to identify animals susceptible to toxicity from ivermectin and other neurotoxic compounds that interact with the P-gp transport protein. Also provided are whole-animal and cell-based model systems for studying compound interactions with P-gp using the mdr1 truncation mutation described herein. It will be apparent that the precise details of the methods described may be varied or modified without departing from the spirit of the described invention. We claim all such modifications and variations that fall within the scope and spirit of the claims below.

                   #             SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 10 <210> SEQ ID NO 1 <211> LENGTH: 4317 <212> TYPE: DNA <213> ORGANISM: Canis familiaris <220> FEATURE: <221> NAME/KEY: CDS <222> LOCATION: (70)..(3912) <223> OTHER INFORMATION: <400> SEQUENCE: 1 ctaagtcgga gtatcttctt cccaaattcc cttctcggtg gaggttgcga ag #gaaagccc     60 gaggtgacg atg gat cct gaa gga ggc cgt aag ggg # agt gca gag aag aac    111           Met Asp Pro Glu Gly  #Gly Arg Lys Gly Ser Ala Glu Lys Asn           1         #       5            #        10 ttc tgg aaa atg ggc aaa aaa agt aaa aaa ga #g aag aaa gaa aag aaa      159 Phe Trp Lys Met Gly Lys Lys Ser Lys Lys Gl #u Lys Lys Glu Lys Lys 15                   #20                   #25                   #30 cca act gtc agc acg ttt gca atg ttt cgc ta #t tca aat tgg ctt gat      207 Pro Thr Val Ser Thr Phe Ala Met Phe Arg Ty #r Ser Asn Trp Leu Asp                 35   #                40   #                45 agg ttg tat atg ttg gtg ggg aca atg gct gc #c atc atc cat gga gct      255 Arg Leu Tyr Met Leu Val Gly Thr Met Ala Al #a Ile Ile His Gly Ala             50       #            55       #            60 gca ctc cct ctc atg atg ctg gtt ttt gga aa #c atg aca gat agc ttt      303 Ala Leu Pro Leu Met Met Leu Val Phe Gly As #n Met Thr Asp Ser Phe         65           #        70           #        75 gca aat gca gga att tca aga aac aaa act tt #t cca gtt ata att aat      351 Ala Asn Ala Gly Ile Ser Arg Asn Lys Thr Ph #e Pro Val Ile Ile Asn     80               #    85               #    90 gaa agt att acg aac aat aca caa cat ttc at #c aac cat ctg gag gag      399 Glu Ser Ile Thr Asn Asn Thr Gln His Phe Il #e Asn His Leu Glu Glu 95                   #100                  #105                  #110 gaa atg acc acg tat gcc tat tat tac agt gg #g atc ggt gct ggc gtg      447 Glu Met Thr Thr Tyr Ala Tyr Tyr Tyr Ser Gl #y Ile Gly Ala Gly Val                 115   #               120   #               125 ctg gtg gct gct tac atc cag gtt tca ttc tg #g tgc ctg gca gca gga      495 Leu Val Ala Ala Tyr Ile Gln Val Ser Phe Tr #p Cys Leu Ala Ala Gly             130       #           135       #           140 aga cag ata ctc aaa att aga aaa caa ttt tt #t cat gct atc atg cga      543 Arg Gln Ile Leu Lys Ile Arg Lys Gln Phe Ph #e His Ala Ile Met Arg         145           #       150           #       155 cag gag att ggc tgg ttt gac gtg cat gac gt #t ggg gag ctt aac acc      591 Gln Glu Ile Gly Trp Phe Asp Val His Asp Va #l Gly Glu Leu Asn Thr     160               #   165               #   170 cgg ctc aca gac gat gtc tcc aaa atc aat ga #a gga att ggc gac aaa      639 Arg Leu Thr Asp Asp Val Ser Lys Ile Asn Gl #u Gly Ile Gly Asp Lys 175                 1 #80                 1 #85                 1 #90 gtt gga atg ttc ttt caa tca ata gca aca tt #t ttc acc ggt ttt ata      687 Val Gly Met Phe Phe Gln Ser Ile Ala Thr Ph #e Phe Thr Gly Phe Ile                 195   #               200   #               205 gtg ggg ttt aca cct ggt tgg aag cta acc ct #t gtg att ttg gcc atc      735 Val Gly Phe Thr Pro Gly Trp Lys Leu Thr Le #u Val Ile Leu Ala Ile             210       #           215       #           220 agc cct gtt ctt gga ctt tca gcc gcc atc tg #g gca aag ata cta tct      783 Ser Pro Val Leu Gly Leu Ser Ala Ala Ile Tr #p Ala Lys Ile Leu Ser         225           #       230           #       235 tca ttt act gat aaa gaa ctc ttg gcc tat gc #a aaa gct gga gca gta      831 Ser Phe Thr Asp Lys Glu Leu Leu Ala Tyr Al #a Lys Ala Gly Ala Val     240               #   245               #   250 gct gaa gaa gtc tta gca gca atc aga act gt #g att gcc ttt gga gga      879 Ala Glu Glu Val Leu Ala Ala Ile Arg Thr Va #l Ile Ala Phe Gly Gly 255                 2 #60                 2 #65                 2 #70 caa aag aaa gaa ctt gaa agg tac aac aaa aa #t tta gaa gaa gct aaa      927 Gln Lys Lys Glu Leu Glu Arg Tyr Asn Lys As #n Leu Glu Glu Ala Lys                 275   #               280   #               285 aga att ggg ata aag aaa gct atc acg gcc aa #c att tct att ggt gcc      975 Arg Ile Gly Ile Lys Lys Ala Ile Thr Ala As #n Ile Ser Ile Gly Ala             290       #           295       #           300 gct ttc tta ttg atc tat gca tca tat gct ct #g gct ttc tgg tat ggg     1023 Ala Phe Leu Leu Ile Tyr Ala Ser Tyr Ala Le #u Ala Phe Trp Tyr Gly         305           #       310           #       315 acc tcc ttg gtc ctc tcc agt gaa tat act at #t gga cag gta ctc act     1071 Thr Ser Leu Val Leu Ser Ser Glu Tyr Thr Il #e Gly Gln Val Leu Thr     320               #   325               #   330 gtc ttc ttt tct gta tta att ggg gct ttt ag #t att gga cag gca tcc     1119 Val Phe Phe Ser Val Leu Ile Gly Ala Phe Se #r Ile Gly Gln Ala Ser 335                 3 #40                 3 #45                 3 #50 cca agc att gaa gca ttt gca aac gca aga gg #a gca gct tat gaa atc     1167 Pro Ser Ile Glu Ala Phe Ala Asn Ala Arg Gl #y Ala Ala Tyr Glu Ile                 355   #               360   #               365 ttc aag ata att gac aat aaa cca agc att ga #c agc tat tcg aag agt     1215 Phe Lys Ile Ile Asp Asn Lys Pro Ser Ile As #p Ser Tyr Ser Lys Ser             370       #           375       #           380 gga cat aaa cca gat aat att aag gga aat tt #g gaa ttc aaa aat gtt     1263 Gly His Lys Pro Asp Asn Ile Lys Gly Asn Le #u Glu Phe Lys Asn Val         385           #       390           #       395 cac ttc agt tac cct tct cga aaa gaa gtt aa #g atc tta aag ggt ctc     1311 His Phe Ser Tyr Pro Ser Arg Lys Glu Val Ly #s Ile Leu Lys Gly Leu     400               #   405               #   410 aac ctg aag gtt cag agt ggg cag aca gtg gc #g ctg gtt ggg aac agt     1359 Asn Leu Lys Val Gln Ser Gly Gln Thr Val Al #a Leu Val Gly Asn Ser 415                 4 #20                 4 #25                 4 #30 ggc tgc ggg aag agc acg acc gtg cag ctg at #g cag agg ctc tat gac     1407 Gly Cys Gly Lys Ser Thr Thr Val Gln Leu Me #t Gln Arg Leu Tyr Asp                 435   #               440   #               445 ccc aca gat ggc atg gtc tgt att gat gga ca #g gac att agg acc ata     1455 Pro Thr Asp Gly Met Val Cys Ile Asp Gly Gl #n Asp Ile Arg Thr Ile             450       #           455       #           460 aat gta agg cat ctt cgg gaa att act ggt gt #g gtg agt cag gag cct     1503 Asn Val Arg His Leu Arg Glu Ile Thr Gly Va #l Val Ser Gln Glu Pro         465           #       470           #       475 gtg ttg ttt gcc acc acg ata gct gaa aac at #t cgc tat ggc cgc gaa     1551 Val Leu Phe Ala Thr Thr Ile Ala Glu Asn Il #e Arg Tyr Gly Arg Glu     480               #   485               #   490 aat gtc acc atg gat gag att gag aaa gct gt #t aag gaa gcc aat gcc     1599 Asn Val Thr Met Asp Glu Ile Glu Lys Ala Va #l Lys Glu Ala Asn Ala 495                 5 #00                 5 #05                 5 #10 tat gat ttt atc atg aaa cta cct aat aaa tt #t gac act ctg gtt gga     1647 Tyr Asp Phe Ile Met Lys Leu Pro Asn Lys Ph #e Asp Thr Leu Val Gly                 515   #               520   #               525 gag aga ggg gcc cgg ctg agt ggt gga cag aa #a cag aga atc gcc att     1695 Glu Arg Gly Ala Arg Leu Ser Gly Gly Gln Ly #s Gln Arg Ile Ala Ile             530       #           535       #           540 gct cgg gcc ctg gtt cgc aac ccc aag att ct #t ctg ctg gat gag gca     1743 Ala Arg Ala Leu Val Arg Asn Pro Lys Ile Le #u Leu Leu Asp Glu Ala         545           #       550           #       555 acg tca gct ctg gac act gaa agt gaa gca gt #g gtt cag gtg gcc ctg     1791 Thr Ser Ala Leu Asp Thr Glu Ser Glu Ala Va #l Val Gln Val Ala Leu     560               #   565               #   570 gat aag gcc aga aaa ggc cgg act acc att gt #g ata gct cat cgt ttg     1839 Asp Lys Ala Arg Lys Gly Arg Thr Thr Ile Va #l Ile Ala His Arg Leu 575                 5 #80                 5 #85                 5 #90 tct aca gtt cgt aat gcc gat gtc att gct gg #t ttt gat gat gga gtc     1887 Ser Thr Val Arg Asn Ala Asp Val Ile Ala Gl #y Phe Asp Asp Gly Val                 595   #               600   #               605 att gtg gag aaa gga aat cat gat gaa ctc at #g aaa gag aag ggc att     1935 Ile Val Glu Lys Gly Asn His Asp Glu Leu Me #t Lys Glu Lys Gly Ile             610       #           615       #           620 tac ttc aaa ctt gtc aca atg cag aca aga gg #a aat gaa att gag tta     1983 Tyr Phe Lys Leu Val Thr Met Gln Thr Arg Gl #y Asn Glu Ile Glu Leu         625           #       630           #       635 gaa aat gcc act ggt gaa tcc aaa agt gaa ag #t gat gcc ttg gaa atg     2031 Glu Asn Ala Thr Gly Glu Ser Lys Ser Glu Se #r Asp Ala Leu Glu Met     640               #   645               #   650 tct cca aaa gat tca ggg tcc agt tta ata aa #a aga aga tca act cgc     2079 Ser Pro Lys Asp Ser Gly Ser Ser Leu Ile Ly #s Arg Arg Ser Thr Arg 655                 6 #60                 6 #65                 6 #70 agg agt ata cat gca cca caa ggc caa gac ag #a aag ctt ggt aca aaa     2127 Arg Ser Ile His Ala Pro Gln Gly Gln Asp Ar #g Lys Leu Gly Thr Lys                 675   #               680   #               685 gag gac ttg aat gag aat gtt cct tca gtt tc #c ttc tgg agg att ctg     2175 Glu Asp Leu Asn Glu Asn Val Pro Ser Val Se #r Phe Trp Arg Ile Leu             690       #           695       #           700 aag ctg aac tca act gaa tgg cct tat ttt gt #g gtt ggt ata ttt tgt     2223 Lys Leu Asn Ser Thr Glu Trp Pro Tyr Phe Va #l Val Gly Ile Phe Cys         705           #       710           #       715 gct att ata aac gga ggc ctg caa cca gca tt #t tca ata ata ttt tca     2271 Ala Ile Ile Asn Gly Gly Leu Gln Pro Ala Ph #e Ser Ile Ile Phe Ser     720               #   725               #   730 agg att ata ggg atc ttt acc cga gat gag ga #t cct gaa aca aaa cga     2319 Arg Ile Ile Gly Ile Phe Thr Arg Asp Glu As #p Pro Glu Thr Lys Arg 735                 7 #40                 7 #45                 7 #50 cag aat agt aac atg ttt tct gta ttg ttt ct #a gtc ctt gga att att     2367 Gln Asn Ser Asn Met Phe Ser Val Leu Phe Le #u Val Leu Gly Ile Ile                 755   #               760   #               765 tct ttt att aca ttt ttc ctc cag ggc ttc ac #a ttt ggc aaa gct ggg     2415 Ser Phe Ile Thr Phe Phe Leu Gln Gly Phe Th #r Phe Gly Lys Ala Gly             770       #           775       #           780 gag atc ctc act aag cgg ctt cga tac atg gt #t ttc aga tcc atg ctg     2463 Glu Ile Leu Thr Lys Arg Leu Arg Tyr Met Va #l Phe Arg Ser Met Leu         785           #       790           #       795 aga cag gat gtc agc tgg ttt gat gac cct aa #a aac acc act gga gca     2511 Arg Gln Asp Val Ser Trp Phe Asp Asp Pro Ly #s Asn Thr Thr Gly Ala     800               #   805               #   810 ttg aca acc agg ctt gcc aat gat gcg gct ca #a gtt aaa ggg gct ata     2559 Leu Thr Thr Arg Leu Ala Asn Asp Ala Ala Gl #n Val Lys Gly Ala Ile 815                 8 #20                 8 #25                 8 #30 ggt tcc agg ctt gct gtc att acc cag aat at #a gca aat ctt ggg aca     2607 Gly Ser Arg Leu Ala Val Ile Thr Gln Asn Il #e Ala Asn Leu Gly Thr                 835   #               840   #               845 ggc att att ata tcc tta atc tat ggt tgg ca #a tta aca ctt tta ctc     2655 Gly Ile Ile Ile Ser Leu Ile Tyr Gly Trp Gl #n Leu Thr Leu Leu Leu             850       #           855       #           860 tta gca att gta ccc atc att gca ata gca gg #a gtt gtt gaa atg aaa     2703 Leu Ala Ile Val Pro Ile Ile Ala Ile Ala Gl #y Val Val Glu Met Lys         865           #       870           #       875 atg ttg tct gga caa gca ctg aaa gat aag aa #a gag cta gaa gga gct     2751 Met Leu Ser Gly Gln Ala Leu Lys Asp Lys Ly #s Glu Leu Glu Gly Ala     880               #   885               #   890 ggg aag att gct aca gaa gcc atc gaa aac tt #c cga act gtt gtt tct     2799 Gly Lys Ile Ala Thr Glu Ala Ile Glu Asn Ph #e Arg Thr Val Val Ser 895                 9 #00                 9 #05                 9 #10 ttg act cgg gag cag aag ttt gaa tac atg ta #t gca cag agt ttg caa     2847 Leu Thr Arg Glu Gln Lys Phe Glu Tyr Met Ty #r Ala Gln Ser Leu Gln                 915   #               920   #               925 gta cca tac aga aac tct ttg agg aaa gca ca #c atc ttc ggg gtc tca     2895 Val Pro Tyr Arg Asn Ser Leu Arg Lys Ala Hi #s Ile Phe Gly Val Ser             930       #           935       #           940 ttt tct atc acc cag gca atg atg tat ttt tc #c tat gct ggc tgt ttc     2943 Phe Ser Ile Thr Gln Ala Met Met Tyr Phe Se #r Tyr Ala Gly Cys Phe         945           #       950           #       955 cgg ttt ggt gcc tac ttg gtg gca aat gag tt #c atg aac ttt cag gat     2991 Arg Phe Gly Ala Tyr Leu Val Ala Asn Glu Ph #e Met Asn Phe Gln Asp     960               #   965               #   970 gtt ctt ttg gta ttc tca gct att gtc ttt gg #t gcc atg gca gtg ggg     3039 Val Leu Leu Val Phe Ser Ala Ile Val Phe Gl #y Ala Met Ala Val Gly 975                 9 #80                 9 #85                 9 #90 cag gtc agt tca ttt gct cct gac tat gcc   #aaa gcc aaa gta tca  gca   3087 Gln Val Ser Ser Phe Ala Pro Asp Tyr Ala   #Lys Ala Lys Val Ser  Ala                 995   #               1000   #               1005 gcc cac gtc atc  atg atc att gaa aaa  a #gc cct ctg att gac  agc      3132 Ala His Val Ile  Met Ile Ile Glu Lys  S #er Pro Leu Ile Asp  Ser             1010      #            1015      #            1020 tac agc cct cac  ggc ctc aag cca aat  a #cg ttg gaa gga aat  gtg      3177 Tyr Ser Pro His  Gly Leu Lys Pro Asn  T #hr Leu Glu Gly Asn  Val             1025      #            1030      #            1035 aca ttt aat gag  gtc gtg ttc aac tat  c #cc act cga cca gac  atc      3222 Thr Phe Asn Glu  Val Val Phe Asn Tyr  P #ro Thr Arg Pro Asp  Ile             1040      #            1045      #            1050 ccc gtg ctc cag  ggg ctg agc ctc gag  g #tg aag aag ggc cag  acg      3267 Pro Val Leu Gln  Gly Leu Ser Leu Glu  V #al Lys Lys Gly Gln  Thr             1055      #            1060      #            1065 ctg gcc ctc gta  ggt agc agt ggc tgt  g #gg aag agc aca gtt  gtt      3312 Leu Ala Leu Val  Gly Ser Ser Gly Cys  G #ly Lys Ser Thr Val  Val             1070      #            1075      #            1080 cag ctc cta gag  cgc ttc tat gac ccc  t #tg gct ggt tca gtg  cta      3357 Gln Leu Leu Glu  Arg Phe Tyr Asp Pro  L #eu Ala Gly Ser Val  Leu             1085      #            1090      #            1095 att gat ggc aaa  gag ata aag cac ctg  a #at gtc cag tgg ctc  cga      3402 Ile Asp Gly Lys  Glu Ile Lys His Leu  A #sn Val Gln Trp Leu  Arg             1100      #            1105      #            1110 gca cac ctg ggc  atc gtg tct cag gag  c #cc atc ctg ttt gac  tgc      3447 Ala His Leu Gly  Ile Val Ser Gln Glu  P #ro Ile Leu Phe Asp  Cys             1115      #            1120      #            1125 agc att gcc gag  aac att gcc tat gga  g #ac aac agc cgg gtc  gta      3492 Ser Ile Ala Glu  Asn Ile Ala Tyr Gly  A #sp Asn Ser Arg Val  Val             1130      #            1135      #            1140 tca cat gaa gag  att atg cag gca gcc  a #ag gag gcc aac ata  cac      3537 Ser His Glu Glu  Ile Met Gln Ala Ala  L #ys Glu Ala Asn Ile  His             1145      #            1150      #            1155 cac ttc atc gag  aca ctc cct gag aaa  t #ac aac acc aga gta  gga      3582 His Phe Ile Glu  Thr Leu Pro Glu Lys  T #yr Asn Thr Arg Val  Gly             1160      #            1165      #            1170 gac aaa gga acc  cag ctc tct ggt ggc  c #ag aaa cag cgc att  gcc      3627 Asp Lys Gly Thr  Gln Leu Ser Gly Gly  G #ln Lys Gln Arg Ile  Ala             1175      #            1180      #            1185 ata gct cgc gct  ctt gtt aga cag cct  c #at att ttg ctt ttg  gat      3672 Ile Ala Arg Ala  Leu Val Arg Gln Pro  H #is Ile Leu Leu Leu  Asp             1190      #            1195      #            1200 gaa gct aca tca  gct ctg gat aca gaa  a #gt gaa aag gtt gtc  caa      3717 Glu Ala Thr Ser  Ala Leu Asp Thr Glu  S #er Glu Lys Val Val  Gln             1205      #            1210      #            1215 gaa gcc ctg gac  aaa gcc aga gaa ggc  c #gc acc tgc att gtg  atc      3762 Glu Ala Leu Asp  Lys Ala Arg Glu Gly  A #rg Thr Cys Ile Val  Ile             1220      #            1225      #            1230 gcc cac cgc ttg  tcc acc atc cag aat  g #ca gat tta ata gtg  gtg      3807 Ala His Arg Leu  Ser Thr Ile Gln Asn  A #la Asp Leu Ile Val  Val             1235      #            1240      #            1245 ttt cag aat ggc  aaa gtc aag gag cat  g #gc aca cat caa cag  ctg      3852 Phe Gln Asn Gly  Lys Val Lys Glu His  G #ly Thr His Gln Gln  Leu             1250      #            1255      #            1260 ctg gct cag aaa  ggc atc tat ttt tcc  a #tg atc agt gtc cag  gct      3897 Leu Ala Gln Lys  Gly Ile Tyr Phe Ser  M #et Ile Ser Val Gln  Ala             1265      #            1270      #            1275 gga gca aag cgc  tag tgaactgtgg ccatatgagc tgtta #aatat tttttaatat    3952 Gly Ala Lys Arg             1280 ttgtgttaaa acatggcatt taatcaaagt taaaaggtga gcacttactg ga #aaaactat   4012 gtagaactac ctgtttaaca tttcttgctg caactgaaga tcattccacc aa #gttcagag   4072 tcttcagatt ttataattaa aggaaccaaa agaaacatta tctgatggaa ta #aaatattg   4132 gtgttaattg cattataaaa ttatagagta attcaaagta gattttgtta at #aaattgta   4192 taatttttgt ttatatttta tttgtaactt actgctttgc tgaaagatta ta #gaagtggt   4252 aaaaagtact gaatgtttga ataaagtgct agctataata aaactaaact tt #tatatgaa   4312 aaaaa                  #                   #                   #          4317 <210> SEQ ID NO 2 <211> LENGTH: 1280 <212> TYPE: PRT <213> ORGANISM: Canis familiaris <400> SEQUENCE: 2 Met Asp Pro Glu Gly Gly Arg Lys Gly Ser Al #a Glu Lys Asn Phe Trp 1               5    #                10   #                15 Lys Met Gly Lys Lys Ser Lys Lys Glu Lys Ly #s Glu Lys Lys Pro Thr             20       #            25       #            30 Val Ser Thr Phe Ala Met Phe Arg Tyr Ser As #n Trp Leu Asp Arg Leu         35           #        40           #        45 Tyr Met Leu Val Gly Thr Met Ala Ala Ile Il #e His Gly Ala Ala Leu     50               #    55               #    60 Pro Leu Met Met Leu Val Phe Gly Asn Met Th #r Asp Ser Phe Ala Asn 65                   #70                   #75                   #80 Ala Gly Ile Ser Arg Asn Lys Thr Phe Pro Va #l Ile Ile Asn Glu Ser                 85   #                90   #                95 Ile Thr Asn Asn Thr Gln His Phe Ile Asn Hi #s Leu Glu Glu Glu Met             100       #           105       #           110 Thr Thr Tyr Ala Tyr Tyr Tyr Ser Gly Ile Gl #y Ala Gly Val Leu Val         115           #       120           #       125 Ala Ala Tyr Ile Gln Val Ser Phe Trp Cys Le #u Ala Ala Gly Arg Gln     130               #   135               #   140 Ile Leu Lys Ile Arg Lys Gln Phe Phe His Al #a Ile Met Arg Gln Glu 145                 1 #50                 1 #55                 1 #60 Ile Gly Trp Phe Asp Val His Asp Val Gly Gl #u Leu Asn Thr Arg Leu                 165   #               170   #               175 Thr Asp Asp Val Ser Lys Ile Asn Glu Gly Il #e Gly Asp Lys Val Gly             180       #           185       #           190 Met Phe Phe Gln Ser Ile Ala Thr Phe Phe Th #r Gly Phe Ile Val Gly         195           #       200           #       205 Phe Thr Pro Gly Trp Lys Leu Thr Leu Val Il #e Leu Ala Ile Ser Pro     210               #   215               #   220 Val Leu Gly Leu Ser Ala Ala Ile Trp Ala Ly #s Ile Leu Ser Ser Phe 225                 2 #30                 2 #35                 2 #40 Thr Asp Lys Glu Leu Leu Ala Tyr Ala Lys Al #a Gly Ala Val Ala Glu                 245   #               250   #               255 Glu Val Leu Ala Ala Ile Arg Thr Val Ile Al #a Phe Gly Gly Gln Lys             260       #           265       #           270 Lys Glu Leu Glu Arg Tyr Asn Lys Asn Leu Gl #u Glu Ala Lys Arg Ile         275           #       280           #       285 Gly Ile Lys Lys Ala Ile Thr Ala Asn Ile Se #r Ile Gly Ala Ala Phe     290               #   295               #   300 Leu Leu Ile Tyr Ala Ser Tyr Ala Leu Ala Ph #e Trp Tyr Gly Thr Ser 305                 3 #10                 3 #15                 3 #20 Leu Val Leu Ser Ser Glu Tyr Thr Ile Gly Gl #n Val Leu Thr Val Phe                 325   #               330   #               335 Phe Ser Val Leu Ile Gly Ala Phe Ser Ile Gl #y Gln Ala Ser Pro Ser             340       #           345       #           350 Ile Glu Ala Phe Ala Asn Ala Arg Gly Ala Al #a Tyr Glu Ile Phe Lys         355           #       360           #       365 Ile Ile Asp Asn Lys Pro Ser Ile Asp Ser Ty #r Ser Lys Ser Gly His     370               #   375               #   380 Lys Pro Asp Asn Ile Lys Gly Asn Leu Glu Ph #e Lys Asn Val His Phe 385                 3 #90                 3 #95                 4 #00 Ser Tyr Pro Ser Arg Lys Glu Val Lys Ile Le #u Lys Gly Leu Asn Leu                 405   #               410   #               415 Lys Val Gln Ser Gly Gln Thr Val Ala Leu Va #l Gly Asn Ser Gly Cys             420       #           425       #           430 Gly Lys Ser Thr Thr Val Gln Leu Met Gln Ar #g Leu Tyr Asp Pro Thr         435           #       440           #       445 Asp Gly Met Val Cys Ile Asp Gly Gln Asp Il #e Arg Thr Ile Asn Val     450               #   455               #   460 Arg His Leu Arg Glu Ile Thr Gly Val Val Se #r Gln Glu Pro Val Leu 465                 4 #70                 4 #75                 4 #80 Phe Ala Thr Thr Ile Ala Glu Asn Ile Arg Ty #r Gly Arg Glu Asn Val                 485   #               490   #               495 Thr Met Asp Glu Ile Glu Lys Ala Val Lys Gl #u Ala Asn Ala Tyr Asp             500       #           505       #           510 Phe Ile Met Lys Leu Pro Asn Lys Phe Asp Th #r Leu Val Gly Glu Arg         515           #       520           #       525 Gly Ala Arg Leu Ser Gly Gly Gln Lys Gln Ar #g Ile Ala Ile Ala Arg     530               #   535               #   540 Ala Leu Val Arg Asn Pro Lys Ile Leu Leu Le #u Asp Glu Ala Thr Ser 545                 5 #50                 5 #55                 5 #60 Ala Leu Asp Thr Glu Ser Glu Ala Val Val Gl #n Val Ala Leu Asp Lys                 565   #               570   #               575 Ala Arg Lys Gly Arg Thr Thr Ile Val Ile Al #a His Arg Leu Ser Thr             580       #           585       #           590 Val Arg Asn Ala Asp Val Ile Ala Gly Phe As #p Asp Gly Val Ile Val         595           #       600           #       605 Glu Lys Gly Asn His Asp Glu Leu Met Lys Gl #u Lys Gly Ile Tyr Phe     610               #   615               #   620 Lys Leu Val Thr Met Gln Thr Arg Gly Asn Gl #u Ile Glu Leu Glu Asn 625                 6 #30                 6 #35                 6 #40 Ala Thr Gly Glu Ser Lys Ser Glu Ser Asp Al #a Leu Glu Met Ser Pro                 645   #               650   #               655 Lys Asp Ser Gly Ser Ser Leu Ile Lys Arg Ar #g Ser Thr Arg Arg Ser             660       #           665       #           670 Ile His Ala Pro Gln Gly Gln Asp Arg Lys Le #u Gly Thr Lys Glu Asp         675           #       680           #       685 Leu Asn Glu Asn Val Pro Ser Val Ser Phe Tr #p Arg Ile Leu Lys Leu     690               #   695               #   700 Asn Ser Thr Glu Trp Pro Tyr Phe Val Val Gl #y Ile Phe Cys Ala Ile 705                 7 #10                 7 #15                 7 #20 Ile Asn Gly Gly Leu Gln Pro Ala Phe Ser Il #e Ile Phe Ser Arg Ile                 725   #               730   #               735 Ile Gly Ile Phe Thr Arg Asp Glu Asp Pro Gl #u Thr Lys Arg Gln Asn             740       #           745       #           750 Ser Asn Met Phe Ser Val Leu Phe Leu Val Le #u Gly Ile Ile Ser Phe         755           #       760           #       765 Ile Thr Phe Phe Leu Gln Gly Phe Thr Phe Gl #y Lys Ala Gly Glu Ile     770               #   775               #   780 Leu Thr Lys Arg Leu Arg Tyr Met Val Phe Ar #g Ser Met Leu Arg Gln 785                 7 #90                 7 #95                 8 #00 Asp Val Ser Trp Phe Asp Asp Pro Lys Asn Th #r Thr Gly Ala Leu Thr                 805   #               810   #               815 Thr Arg Leu Ala Asn Asp Ala Ala Gln Val Ly #s Gly Ala Ile Gly Ser             820       #           825       #           830 Arg Leu Ala Val Ile Thr Gln Asn Ile Ala As #n Leu Gly Thr Gly Ile         835           #       840           #       845 Ile Ile Ser Leu Ile Tyr Gly Trp Gln Leu Th #r Leu Leu Leu Leu Ala     850               #   855               #   860 Ile Val Pro Ile Ile Ala Ile Ala Gly Val Va #l Glu Met Lys Met Leu 865                 8 #70                 8 #75                 8 #80 Ser Gly Gln Ala Leu Lys Asp Lys Lys Glu Le #u Glu Gly Ala Gly Lys                 885   #               890   #               895 Ile Ala Thr Glu Ala Ile Glu Asn Phe Arg Th #r Val Val Ser Leu Thr             900       #           905       #           910 Arg Glu Gln Lys Phe Glu Tyr Met Tyr Ala Gl #n Ser Leu Gln Val Pro         915           #       920           #       925 Tyr Arg Asn Ser Leu Arg Lys Ala His Ile Ph #e Gly Val Ser Phe Ser     930               #   935               #   940 Ile Thr Gln Ala Met Met Tyr Phe Ser Tyr Al #a Gly Cys Phe Arg Phe 945                 9 #50                 9 #55                 9 #60 Gly Ala Tyr Leu Val Ala Asn Glu Phe Met As #n Phe Gln Asp Val Leu                 965   #               970   #               975 Leu Val Phe Ser Ala Ile Val Phe Gly Ala Me #t Ala Val Gly Gln Val             980       #           985       #           990 Ser Ser Phe Ala Pro Asp Tyr Ala  Lys Ala  #Lys Val Ser  Ala Ala His         995           #       1000           #       1005 Val Ile  Met Ile Ile Glu Lys  Ser Pro L #eu Ile Asp  Ser Tyr Ser     1010              #    1015              #    1020 Pro His  Gly Leu Lys Pro Asn  Thr Leu G #lu Gly Asn  Val Thr Phe     1025              #    1030              #    1035 Asn Glu  Val Val Phe Asn Tyr  Pro Thr A #rg Pro Asp  Ile Pro Val     1040              #    1045              #    1050 Leu Gln  Gly Leu Ser Leu Glu  Val Lys L #ys Gly Gln  Thr Leu Ala     1055              #    1060              #    1065 Leu Val  Gly Ser Ser Gly Cys  Gly Lys S #er Thr Val  Val Gln Leu     1070              #    1075              #    1080 Leu Glu  Arg Phe Tyr Asp Pro  Leu Ala G #ly Ser Val  Leu Ile Asp     1085              #    1090              #    1095 Gly Lys  Glu Ile Lys His Leu  Asn Val G #ln Trp Leu  Arg Ala His     1100              #    1105              #    1110 Leu Gly  Ile Val Ser Gln Glu  Pro Ile L #eu Phe Asp  Cys Ser Ile     1115              #    1120              #    1125 Ala Glu  Asn Ile Ala Tyr Gly  Asp Asn S #er Arg Val  Val Ser His     1130              #    1135              #    1140 Glu Glu  Ile Met Gln Ala Ala  Lys Glu A #la Asn Ile  His His Phe     1145              #    1150              #    1155 Ile Glu  Thr Leu Pro Glu Lys  Tyr Asn T #hr Arg Val  Gly Asp Lys     1160              #    1165              #    1170 Gly Thr  Gln Leu Ser Gly Gly  Gln Lys G #ln Arg Ile  Ala Ile Ala     1175              #    1180              #    1185 Arg Ala  Leu Val Arg Gln Pro  His Ile L #eu Leu Leu  Asp Glu Ala     1190              #    1195              #    1200 Thr Ser  Ala Leu Asp Thr Glu  Ser Glu L #ys Val Val  Gln Glu Ala     1205              #    1210              #    1215 Leu Asp  Lys Ala Arg Glu Gly  Arg Thr C #ys Ile Val  Ile Ala His     1220              #    1225              #    1230 Arg Leu  Ser Thr Ile Gln Asn  Ala Asp L #eu Ile Val  Val Phe Gln     1235              #    1240              #    1245 Asn Gly  Lys Val Lys Glu His  Gly Thr H #is Gln Gln  Leu Leu Ala     1250              #    1255              #    1260 Gln Lys  Gly Ile Tyr Phe Ser  Met Ile S #er Val Gln  Ala Gly Ala     1265              #    1270              #    1275 Lys Arg     1280 <210> SEQ ID NO 3 <211> LENGTH: 20 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 3 tccggtttgg tgcctacttg             #                   #                   # 20 <210> SEQ ID NO 4 <211> LENGTH: 21 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 4 tgctccttga ctttgccatt c            #                   #                   #21 <210> SEQ ID NO 5 <211> LENGTH: 22 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 5 cctcactaag cggcttcgat ac            #                   #                 22 <210> SEQ ID NO 6 <211> LENGTH: 22 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 6 aaacaggatg ggctcctgag ac            #                   #                 22 <210> SEQ ID NO 7 <211> LENGTH: 20 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 7 cagcacgttt gcaatgtttc             #                   #                   # 20 <210> SEQ ID NO 8 <211> LENGTH: 22 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 8 tctggtttat gtccactctt cg            #                   #                 22 <210> SEQ ID NO 9 <211> LENGTH: 21 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 9 aggcatcccc aagcattgaa g            #                   #                   #21 <210> SEQ ID NO 10 <211> LENGTH: 20 <212> TYPE: DNA <213> ORGANISM: synthetic oligonucleotide <400> SEQUENCE: 10 tgagccgcat cattggcaag             #                   #                   # 20 

We claim:
 1. A method of detecting ivermectin sensitivity in a canine subject, comprising determining whether a gale-truncation mutation in a mdr1-encoding sequence of the canine subject is present in the canine subject, wherein the gene truncation mutation is a deletion of four base pairs at about residue 294-297 of SEQ ID NO: 1, wherein presence of the gene-truncation mutation indicates that the subject is sensitive to ivermectin.
 2. The method of claim 1, wherein the method is used to evaluate whether the canine subject can be treated safely with ivermectin or another drug that can be excluded from a cell or an organ by P-gp.
 3. The method of claim 2, wherein the method is used to evaluate whether the canine subject can be treated safely with ivermectin or another drug that can be excluded from the brain by P-gp.
 4. The method of claim 1, further comprising determining whether the canine subject is homozygous or heterozygous for the gene-truncation mutation.
 5. The method of claim 1, wherein determining whether a gene-truncation mutation is present in the canine subject comprises subjecting DNA or RNA from the subject to amplification using oligonucleotide primers.
 6. The method of claim 4, comprising an oligonucleotide ligation assay.
 7. The method of claim 1, comprising: obtaining a test sample of DNA containing a mdr1 sequence of the canine subject; end determining whether the mdr1 sequence of the canine subject has the gene-truncation mutation in the mdr1 sequence, wherein the presence of the mutation indicates sensitivity of the canine subject to ivermectin.
 8. The method of claim 7, wherein determining whether the mdr1 sequence of the canine subject has the mutation comprises using restriction digestion, probe hybridization, nucleic acid amplification, or nucleotide sequencing.
 9. The method of claim 1, comprising: obtaining from the canine subject a test sample of DNA; contacting the test sample with at least one nucleic acid probe for the mdr1 gene truncation mutation that is associated with ivermectin sensitivity, to form a hybridization sample; maintaining the hybridization sample under conditions sufficient for specific hybridization of the mdr1 sequence with the nucleic acid probe; and detecting whether the mdr1 sequence specifically hybridizes with the nucleic acid probe, wherein specific hybridization of the mdr1 sequence with the nucleic acid probe indicates ivermectin sensitivity of the canine subject.
 10. The method of claim 8, wherein the probe is present on a substrate.
 11. The method of claim 10, wherein the substrate is a nucleotide array. 